From b38fdc7112e411fcaf22b77e7a7335604e1a291c Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Thu, 29 Oct 2026 13:24:37 +0100 Subject: [PATCH 1/3] Clear pipeline-level nf-core lint warnings, bump to 1.2.0dev - manifest.version 1.1.0 -> 1.2.0dev; snapshot version keys follow - move the 13 flat subworkflows/local/*.nf files to /main.nf (includes one level deeper; explicit .nf paths in paired/, tumor_only/ and the tests updated) - skip_modkit moved into skip_options; descriptions for generate_gvcf, autocorrelation, vep_custom, vep_custom_tbi, severus_minsupport and wakhan_chroms - resolve template TODOs: pipeline citation in the methods description, pipeline-specific contribution guidelines, and drop comments whose work was already done - remove lint_log.txt, a lint debug log committed by mistake - RO-Crate regenerated Co-Authored-By: Claude Opus 5.5 --- CHANGELOG.md | 1 + README.md | 3 - assets/methods_description_template.yml | 4 +- conf/base.config | 2 - docs/CONTRIBUTING.md | 6 +- lint_log.txt | 3596 ----------------- modules/local/cramino/meta.yml | 1 - .../matrixgenerator/tests/main.nf.test | 2 +- nextflow.config | 4 +- nextflow_schema.json | 29 +- ro-crate-metadata.json | 20 +- .../{deepsomatic.nf => deepsomatic/main.nf} | 6 +- subworkflows/local/{dmr.nf => dmr/main.nf} | 8 +- .../local/{ecdna.nf => ecdna/main.nf} | 12 +- .../local/{fiberseq.nf => fiberseq/main.nf} | 8 +- .../main.nf} | 4 +- .../local/paired/paired_smallvar_germline.nf | 2 +- .../local/paired/paired_smallvar_somatic.nf | 4 +- .../main.nf} | 36 +- .../main.nf} | 4 +- .../main.nf} | 2 +- .../main.nf} | 14 +- .../main.nf} | 4 +- .../main.nf} | 14 +- .../main.nf} | 6 +- .../main.nf} | 16 +- subworkflows/local/tests/dmr.nf.test | 2 +- subworkflows/local/tests/ecdna.nf.test | 2 +- .../local/tests/padfoot_annotation.nf.test | 2 +- .../local/tests/prepare_aa_data_repo.nf.test | 2 +- .../local/tests/prepare_signatures.nf.test | 2 +- .../local/tests/reconplot_figures.nf.test | 2 +- .../local/tumor_only/tumoronly_smallvar.nf | 6 +- tests/chm13.nf.test.snap | 2 +- tests/clair_only.nf.test.snap | 2 +- tests/consensus.nf.test.snap | 2 +- tests/deep_only.nf.test.snap | 2 +- tests/default.nf.test.snap | 2 +- tests/nextflow.config | 2 - tests/union.nf.test.snap | 2 +- 40 files changed, 122 insertions(+), 3718 deletions(-) delete mode 100644 lint_log.txt rename subworkflows/local/{deepsomatic.nf => deepsomatic/main.nf} (90%) rename subworkflows/local/{dmr.nf => dmr/main.nf} (92%) rename subworkflows/local/{ecdna.nf => ecdna/main.nf} (91%) rename subworkflows/local/{fiberseq.nf => fiberseq/main.nf} (93%) rename subworkflows/local/{padfoot_annotation.nf => padfoot_annotation/main.nf} (94%) rename subworkflows/local/{phasing_haplotyping.nf => phasing_haplotyping/main.nf} (95%) rename subworkflows/local/{prepare_aa_data_repo.nf => prepare_aa_data_repo/main.nf} (92%) rename subworkflows/local/{prepare_annotation.nf => prepare_annotation/main.nf} (96%) rename subworkflows/local/{prepare_reference_files.nf => prepare_reference_files/main.nf} (93%) rename subworkflows/local/{prepare_signatures.nf => prepare_signatures/main.nf} (94%) rename subworkflows/local/{prepare_vep_plugins.nf => prepare_vep_plugins/main.nf} (86%) rename subworkflows/local/{reconplot_figures.nf => reconplot_figures/main.nf} (94%) rename subworkflows/local/{small_variant_consensus.nf => small_variant_consensus/main.nf} (96%) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0cc8011b..6cf736d6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- [#PR](https://github.com/IntGenomicsLab/lrsomatic/pull/PR) - Cleared the pipeline-level nf-core lint warnings. `manifest.version` is now `1.2.0dev`; the 13 flat `subworkflows/local/*.nf` files moved to `subworkflows/local//main.nf`; `skip_modkit` is in the skip options group and six parameters got schema descriptions; template TODOs are resolved, including a pipeline citation in the MultiQC methods description and pipeline-specific contribution guidelines; and the stray `lint_log.txt` debug log is removed (@ljwharbers). - [#224](https://github.com/IntGenomicsLab/lrsomatic/pull/224) - Updated to the nf-core template for [nf-core/tools 4.2.1](https://github.com/nf-core/tools/releases/tag/4.2.1). Bumps nf-schema to 2.7.3 (needed for Nextflow 26.04) and nft-utils to 1.2.1, sets `manifest.diagram` to the existing metro map (`assets/lrsomatic_1.0.png`), replaces `fix_linting.yml` with the reusable `fix-linting.yml` from nf-core/actions, adds recommended VS Code extensions, and stops `workflow.onComplete` from blocking on the MultiQC report. The linting workflow keeps running plain `pre-commit` rather than the template's prek-action (@ljwharbers). - [#224](https://github.com/IntGenomicsLab/lrsomatic/pull/224) - Dropped `ext.use_gpu` from the GPU resource labels, following the template: `task.accelerator` now decides GPU use, and `CLAIR3` reads it instead of `task.ext.use_gpu` (@ljwharbers). - [#204](https://github.com/IntGenomicsLab/lrsomatic/pull/204) - With `--modkit_phased` set and haplotype DMR running, `5hmC` is appended to `--modified-bases` whenever `--modkit_args` names `5mC` without it, so the published `modkit_pileup/*_{hp1,hp2,combined}.bed.gz` now carry a 5hmC row next to each 5mC row. `modkit dmr pair` rejects bedMethyl rows whose valid coverage includes uncounted (`N_other`) calls, which ONT SUP data calling both 5mC and 5hmC produces under the `--cpg --modified-bases 5mC` default. Runs with `--skip_dmr`, without `--modkit_phased`, or without DMR references keep `--modkit_args` exactly as given (@YannVRB). diff --git a/README.md b/README.md index a8387f74..90ec15e0 100644 --- a/README.md +++ b/README.md @@ -72,9 +72,6 @@ c. Somatic SV and CNA functional annotation ([`Padfoot`](https://github.com/Kolm a. Rearrangement and copy-number figures per CN/SV caller pair ([`ReConPlot`](https://github.com/cortes-ciriano-lab/ReConPlot)) - - ## Usage > [!NOTE] diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index fca23d8a..c157bc19 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -3,16 +3,16 @@ description: "Suggested text and references to use when describing pipeline usag section_name: "IntGenomicsLab/lrsomatic Methods Description" section_href: "https://github.com/IntGenomicsLab/lrsomatic" plot_type: "html" -## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline ## You inject any metadata in the Nextflow '${workflow}' object data: |

Methods

-

Data was processed using IntGenomicsLab/lrsomatic v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

+

Data was processed using IntGenomicsLab/lrsomatic v${workflow.manifest.version} ${doi_text} (Forsyth, Harbers et al., 2026), built with the nf-core framework (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

${workflow.commandLine}

${tool_citations}

References

    +
  • Forsyth, R. A., Harbers, L., Verhasselt, A., Rocha Iraizós, A.-L., Yang, S., Vande Velde, J., Davies, C., Pillay, N., Lambrechts, L., & Demeulemeester, J. (2026). LRSomatic: a highly scalable and robust pipeline for somatic variant calling in long-read sequencing data. bioRxiv 2026.02.26.707772. doi: 10.64898/2026.02.26.707772
  • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
  • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
  • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
    • diff --git a/conf/base.config b/conf/base.config index c12468aa..dce76426 100644 --- a/conf/base.config +++ b/conf/base.config @@ -10,7 +10,6 @@ process { - // TODO nf-core: Check the defaults for all processes cpus = { 1 * task.attempt } memory = { 6.GB * task.attempt } time = { 4.h * task.attempt } @@ -24,7 +23,6 @@ process { // These labels are used and recognised by default in DSL2 files hosted on nf-core/modules. // If possible, it would be nice to keep the same label naming convention when // adding in your local modules too. - // TODO nf-core: Customise requirements for specific processes. // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors withLabel:process_gpu_high { accelerator = { (params.use_gpu as boolean) ? 1 : null } diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md index 8d7bdfe7..97a76586 100644 --- a/docs/CONTRIBUTING.md +++ b/docs/CONTRIBUTING.md @@ -162,4 +162,8 @@ If you update images or graphics, follow the nf-core [style guidelines](https:// ## Pipeline specific contribution guidelines - +- [ ] Before writing a local module, check whether nf-core/modules already has one, and install it with `nf-core modules install`. +- [ ] Keep the `[ meta, data ]` tuple shape across module and subworkflow boundaries, so sample metadata reaches every downstream step. +- [ ] Put local subworkflows in `subworkflows/local//main.nf`. +- [ ] Add a `CHANGELOG.md` entry with the PR number for every user-facing change. +- [ ] Tag fast (stub) tests with `small`: pull-request CI runs only tests with that tag. The extended pipeline tests (`clair_only`, `consensus`, `deep_only`, `union`) run only on release or manual dispatch, so regenerate their snapshots whenever an output changes. diff --git a/lint_log.txt b/lint_log.txt deleted file mode 100644 index 366aea19..00000000 --- a/lint_log.txt +++ /dev/null @@ -1,3596 +0,0 @@ -[2025-11-27 15:47:39,242] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:47:39,244] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/lustre1/project/stg_00096/home/rforsyth/LRSomatic/lrsomatic, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:47:39,250] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:47:39,251] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:47:39,252] nf_core.utils [DEBUG ] Using config file: .nf-core.yml -[2025-11-27 15:47:39,252] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:47:39,252] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:47:39,254] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:47:39,258] git.cmd [DEBUG ] Popen(['git', 'version'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:47:39,260] git.cmd [DEBUG ] Popen(['git', 'fetch', '-v', '--progress', '--', 'origin'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=True) -[2025-11-27 15:47:40,027] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:47:40,360] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:47:40,375] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:47:40,376] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:47:40,376] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:47:40,378] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:47:40,379] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:47:40,379] nf_core.utils [DEBUG ] Using config file: .nf-core.yml -[2025-11-27 15:47:41,648] nf_core.pipelines.lint_utils [DEBUG ] The following files were modified by prettier: - -modules.json - - -[2025-11-27 15:47:41,651] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:47:41,651] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:47:41,652] nf_core.components.lint [DEBUG ] Registry set to quay.io -[2025-11-27 15:47:41,652] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:47:41,653] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:47:41,705] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:47:41,724] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:47:41,724] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:47:41,725] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:47:41,727] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:47:41,727] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:47:41,728] nf_core.utils [DEBUG ] Using config file: .nf-core.yml -[2025-11-27 15:47:42,155] nf_core.pipelines.lint_utils [DEBUG ] The following files were modified by prettier: - -modules.json - - -[2025-11-27 15:47:42,157] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:47:42,157] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:47:42,158] nf_core.components.lint [DEBUG ] Registry set to quay.io -[2025-11-27 15:47:42,160] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:47:42,160] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:47:42,160] nf_core.utils [DEBUG ] Using config file: .nf-core.yml -[2025-11-27 15:47:42,162] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:47:42,162] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:47:42,163] nf_core.utils [DEBUG ] Using config file: .nf-core.yml -[2025-11-27 15:47:42,163] nf_core.pipelines.lint [INFO ] Testing pipeline: [magenta]. -[2025-11-27 15:47:42,165] nf_core.pipelines.lint [DEBUG ] Running lint test: files_exist -[2025-11-27 15:47:42,167] nf_core.pipelines.lint [DEBUG ] Running lint test: nextflow_config -[2025-11-27 15:47:42,169] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:47:42,169] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:47:42,170] nf_core.utils [DEBUG ] Using config file: .nf-core.yml -[2025-11-27 15:47:42,171] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:47:42,171] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:47:42,171] nf_core.pipelines.schema [DEBUG ] Ignoring parameters from config: ['genomes'] -[2025-11-27 15:47:42,171] nf_core.pipelines.schema [DEBUG ] Ignoring parameters: ['help', 'help_full', 'show_hidden', 'trace_report_suffix', 'genomes'] -[2025-11-27 15:47:42,172] nf_core.pipelines.schema [DEBUG ] JSON file loaded: nextflow_schema.json -[2025-11-27 15:47:42,172] nf_core.pipelines.lint [DEBUG ] Running lint test: nf_test_content -[2025-11-27 15:47:42,173] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:47:42,174] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:47:42,174] nf_core.utils [DEBUG ] Using config file: .nf-core.yml -[2025-11-27 15:47:42,175] nf_core.pipelines.lint [DEBUG ] Running lint test: files_unchanged -[2025-11-27 15:47:42,197] nf_core.utils [DEBUG ] Could not find a config file in the directory '/tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic' -[2025-11-27 15:47:42,378] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:47:42,378] nf_core.utils [DEBUG ] Could not find git hash for pipeline: /tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic. /tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic -[2025-11-27 15:47:42,378] nf_core.utils [DEBUG ] Got '/tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic' as path -[2025-11-27 15:47:42,378] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-2540e072f807b83f582a63138.json -[2025-11-27 15:47:42,379] nf_core.utils [DEBUG ] No conda `environment.yml` file found. -[2025-11-27 15:47:42,382] urllib3.connectionpool [DEBUG ] Starting new HTTPS connection (1): nf-co.re:443 -[2025-11-27 15:47:42,674] urllib3.connectionpool [DEBUG ] https://nf-co.re:443 "GET /pipelines.json HTTP/1.1" 200 None -[2025-11-27 15:47:42,909] nf_core.pipelines.rocrate [DEBUG ] Adding topics: ['nf-core', 'nextflow'] -[2025-11-27 15:47:42,909] nf_core.pipelines.rocrate [DEBUG ] No git repository found. No git contributors will be added as authors. -[2025-11-27 15:47:42,910] nf_core.pipelines.rocrate [INFO ] Saving metadata file to '/tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic' -[2025-11-27 15:47:42,911] nf_core.utils [DEBUG ] Got '/tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic' as path -[2025-11-27 15:47:42,911] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-2540e072f807b83f582a63138.json -[2025-11-27 15:47:42,911] nf_core.utils [DEBUG ] Using config file: /tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic/.nf-core.yml -[2025-11-27 15:47:42,914] nf_core.utils [DEBUG ] Got '/tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic' as path -[2025-11-27 15:47:42,914] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-2540e072f807b83f582a63138.json -[2025-11-27 15:47:42,915] nf_core.utils [DEBUG ] Using config file: /tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic/.nf-core.yml -[2025-11-27 15:47:43,547] nf_core.pipelines.lint_utils [DEBUG ] prettier.................................................................Passed - -[2025-11-27 15:47:43,550] nf_core.pipelines.lint [DEBUG ] Running lint test: actions_nf_test -[2025-11-27 15:47:43,556] nf_core.pipelines.lint [DEBUG ] Running lint test: actions_awstest -[2025-11-27 15:47:43,556] nf_core.pipelines.lint [DEBUG ] Running lint test: actions_awsfulltest -[2025-11-27 15:47:43,556] nf_core.pipelines.lint [DEBUG ] Running lint test: readme -[2025-11-27 15:47:43,557] nf_core.pipelines.lint [DEBUG ] Running lint test: pipeline_todos -[2025-11-27 15:47:43,708] nf_core.pipelines.lint [DEBUG ] Running lint test: pipeline_if_empty_null -[2025-11-27 15:50:35,955] nf_core.pipelines.lint [DEBUG ] Running lint test: plugin_includes -[2025-11-27 15:50:35,958] nf_core.pipelines.lint [DEBUG ] Running lint test: pipeline_name_conventions -[2025-11-27 15:50:35,959] nf_core.pipelines.lint [DEBUG ] Running lint test: template_strings -[2025-11-27 15:50:36,008] nf_core.pipelines.lint [DEBUG ] Running lint test: schema_lint -[2025-11-27 15:50:36,008] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:50:36,009] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:50:36,042] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:50:36,042] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:50:36,043] nf_core.pipelines.lint [DEBUG ] Skipping lint test 'schema_params' -[2025-11-27 15:50:36,043] nf_core.pipelines.lint [DEBUG ] Running lint test: system_exit -[2025-11-27 15:50:36,093] nf_core.pipelines.lint [DEBUG ] Running lint test: schema_description -[2025-11-27 15:50:36,093] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:50:36,093] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:50:36,094] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:50:36,094] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:50:36,125] nf_core.pipelines.lint [DEBUG ] Running lint test: actions_schema_validation -[2025-11-27 15:50:36,126] urllib3.connectionpool [DEBUG ] Starting new HTTPS connection (1): www.schemastore.org:443 -[2025-11-27 15:50:36,292] urllib3.connectionpool [DEBUG ] https://www.schemastore.org:443 "GET /github-workflow HTTP/1.1" 200 14042 -[2025-11-27 15:50:36,454] nf_core.pipelines.lint [DEBUG ] Running lint test: merge_markers -[2025-11-27 15:50:36,514] nf_core.pipelines.lint [DEBUG ] Running lint test: modules_json -[2025-11-27 15:50:36,514] nf_core.pipelines.lint [DEBUG ] Running lint test: multiqc_config -[2025-11-27 15:50:36,516] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:50:36,516] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:50:36,517] nf_core.utils [DEBUG ] Using config file: .nf-core.yml -[2025-11-27 15:50:36,517] nf_core.pipelines.lint [DEBUG ] Running lint test: modules_structure -[2025-11-27 15:50:36,520] nf_core.pipelines.lint [DEBUG ] Running lint test: local_component_structure -[2025-11-27 15:50:36,520] nf_core.pipelines.lint [DEBUG ] Running lint test: base_config -[2025-11-27 15:50:36,522] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:50:36,522] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:50:36,522] nf_core.utils [DEBUG ] Using config file: .nf-core.yml -[2025-11-27 15:50:36,522] nf_core.pipelines.lint.configs [DEBUG ] found sections: [] -[2025-11-27 15:50:36,539] nf_core.pipelines.lint.configs [DEBUG ] found nf_files: ['main.nf', 'workflows/lrsomatic.nf', 'subworkflows/local/tumor_normal_happhase.nf', 'subworkflows/local/tumor_only_happhase.nf', 'subworkflows/local/prepare_annotation.nf', 'subworkflows/local/prepare_reference_files.nf', 'subworkflows/nf-core/utils_nfschema_plugin/main.nf', 'subworkflows/nf-core/bam_stats_samtools/main.nf', 'subworkflows/nf-core/utils_nextflow_pipeline/main.nf', 'subworkflows/nf-core/utils_nfcore_pipeline/main.nf', 'subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf', 'modules/nf-core/ascat/main.nf', 'modules/nf-core/mosdepth/main.nf', 'modules/nf-core/multiqc/main.nf', 'modules/nf-core/wget/main.nf', 'modules/nf-core/unzip/main.nf', 'modules/nf-core/untar/main.nf', 'modules/nf-core/severus/main.nf', 'modules/nf-core/minimap2/align/main.nf', 'modules/nf-core/minimap2/index/main.nf', 'modules/nf-core/bcftools/merge/main.nf', 'modules/nf-core/bcftools/sort/main.nf', 'modules/nf-core/bcftools/concat/main.nf', 'modules/nf-core/modkit/pileup/main.nf', 'modules/nf-core/samtools/idxstats/main.nf', 'modules/nf-core/samtools/faidx/main.nf', 'modules/nf-core/samtools/cat/main.nf', 'modules/nf-core/samtools/index/main.nf', 'modules/nf-core/samtools/stats/main.nf', 'modules/nf-core/samtools/flagstat/main.nf', 'modules/nf-core/longphase/haplotag/main.nf', 'modules/nf-core/longphase/phase/main.nf', 'modules/nf-core/ensemblvep/vep/main.nf', 'modules/nf-core/ensemblvep/download/main.nf', 'modules/nf-core/pigz/uncompress/main.nf', 'modules/local/wakhan/main.nf', 'modules/local/clairs/main.nf', 'modules/local/cramino/main.nf', 'modules/local/metaextract/main.nf', 'modules/local/clairsto/main.nf', 'modules/local/vcfsplit/main.nf', 'modules/local/clair3/main.nf', 'modules/local/fibertoolsrs/fire/main.nf', 'modules/local/fibertoolsrs/predictm6a/main.nf', 'modules/local/fibertoolsrs/qc/main.nf', 'modules/local/fibertoolsrs/nucleosomes/main.nf'] -[2025-11-27 15:50:36,539] nf_core.pipelines.lint [DEBUG ] Running lint test: modules_config -[2025-11-27 15:50:36,541] nf_core.utils [DEBUG ] Got '.' as path -[2025-11-27 15:50:36,541] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json -[2025-11-27 15:50:36,542] nf_core.utils [DEBUG ] Using config file: .nf-core.yml -[2025-11-27 15:50:36,542] nf_core.pipelines.lint.configs [DEBUG ] found sections: ['ENSEMBLVEP_DOWNLOAD'] -[2025-11-27 15:50:36,558] nf_core.pipelines.lint.configs [DEBUG ] found nf_files: ['main.nf', 'workflows/lrsomatic.nf', 'subworkflows/local/tumor_normal_happhase.nf', 'subworkflows/local/tumor_only_happhase.nf', 'subworkflows/local/prepare_annotation.nf', 'subworkflows/local/prepare_reference_files.nf', 'subworkflows/nf-core/utils_nfschema_plugin/main.nf', 'subworkflows/nf-core/bam_stats_samtools/main.nf', 'subworkflows/nf-core/utils_nextflow_pipeline/main.nf', 'subworkflows/nf-core/utils_nfcore_pipeline/main.nf', 'subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf', 'modules/nf-core/ascat/main.nf', 'modules/nf-core/mosdepth/main.nf', 'modules/nf-core/multiqc/main.nf', 'modules/nf-core/wget/main.nf', 'modules/nf-core/unzip/main.nf', 'modules/nf-core/untar/main.nf', 'modules/nf-core/severus/main.nf', 'modules/nf-core/minimap2/align/main.nf', 'modules/nf-core/minimap2/index/main.nf', 'modules/nf-core/bcftools/merge/main.nf', 'modules/nf-core/bcftools/sort/main.nf', 'modules/nf-core/bcftools/concat/main.nf', 'modules/nf-core/modkit/pileup/main.nf', 'modules/nf-core/samtools/idxstats/main.nf', 'modules/nf-core/samtools/faidx/main.nf', 'modules/nf-core/samtools/cat/main.nf', 'modules/nf-core/samtools/index/main.nf', 'modules/nf-core/samtools/stats/main.nf', 'modules/nf-core/samtools/flagstat/main.nf', 'modules/nf-core/longphase/haplotag/main.nf', 'modules/nf-core/longphase/phase/main.nf', 'modules/nf-core/ensemblvep/vep/main.nf', 'modules/nf-core/ensemblvep/download/main.nf', 'modules/nf-core/pigz/uncompress/main.nf', 'modules/local/wakhan/main.nf', 'modules/local/clairs/main.nf', 'modules/local/cramino/main.nf', 'modules/local/metaextract/main.nf', 'modules/local/clairsto/main.nf', 'modules/local/vcfsplit/main.nf', 'modules/local/clair3/main.nf', 'modules/local/fibertoolsrs/fire/main.nf', 'modules/local/fibertoolsrs/predictm6a/main.nf', 'modules/local/fibertoolsrs/qc/main.nf', 'modules/local/fibertoolsrs/nucleosomes/main.nf'] -[2025-11-27 15:50:36,559] nf_core.pipelines.lint [DEBUG ] Running lint test: nfcore_yml -[2025-11-27 15:50:36,563] nf_core.pipelines.lint [DEBUG ] Running lint test: rocrate_readme_sync -[2025-11-27 15:50:36,566] nf_core.components.nfcore_component [DEBUG ] Found 2 inputs in modules/local/wakhan/main.nf -[2025-11-27 15:50:36,566] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'tumor_input': {}}, {'tumor_index': {}}, {'normal_input': {}}, {'normal_index': {}}, {'vcf': {}}, {'breakpoints': {}}], [{'meta2': {}}, {'reference': {}}]] -[2025-11-27 15:50:36,566] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*/*_genes_genome.html") , emit: genes_genome_html - tuple val(meta), path("*/*_genes_genome.pdf") , emit: genes_genome_pdf - tuple val(meta), path("*/*_genome_copynumbers_breakpoints.html") , emit: breakpoints_html - tuple val(meta), path("*/*_genome_copynumbers_breakpoints.pdf") , emit: breakpoints_pdf - tuple val(meta), path("*/*_genome_copynumbers_breakpoints_subclonal.html") , emit: breakpoints_subclonal_html - tuple val(meta), path("*/*_genome_copynumbers_breakpoints_subclonal.pdf") , emit: breakpoints_subclonal_pdf - tuple val(meta), path("*/*_genome_copynumbers_details.html") , emit: copynumbers_details_html - tuple val(meta), path("*/*_genome_copynumbers_details.pdf") , emit: copynumbers_details_pdf - tuple val(meta), path("*/bed_output/*.bed") , emit: bed_files - tuple val(meta), path("*/variation_plots/*.html") , emit: variation_plots - tuple val(meta), path("*/vcf_output/*_wakhan_cna_*.vcf") , emit: vcf_files - tuple val(meta), path("*_heatmap_ploidy_purity.html") , emit: heatmap_html - tuple val(meta), path("*_heatmap_ploidy_purity.html.pdf") , emit: heatmap_pdf - tuple val(meta), path("*_optimized_peak.html") , emit: optimized_peak_html - tuple val(meta), path("coverage_data/*.csv") , emit: coverage_csv - tuple val(meta), path("coverage_plots/*.html") , emit: coverage_plots_html - tuple val(meta), path("coverage_plots/*.pdf") , emit: coverage_plots_pdf - tuple val(meta), path("phasing_output/*.html") , emit: phasing_html - tuple val(meta), path("phasing_output/*.pdf") , emit: phasing_pdf - tuple val(meta), path("phasing_output/*.rephased.vcf.gz") , emit: rephased_vcf - tuple val(meta), path("phasing_output/*.rephased.vcf.gz.csi") , emit: rephased_vcf_index - tuple val(meta), path("snps_loh_plots/*_genome_snps_ratio_loh.html") , emit: snps_loh_plot, optional: true - tuple val(meta), path("solutions_ranks.tsv") , emit: solutions_ranks - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found 24 outputs in modules/local/wakhan/main.nf -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Outputs: {'genes_genome_html': [[{'meta': {}}, {'*/*_genes_genome.html': {}}]], 'genes_genome_pdf': [[{'meta': {}}, {'*/*_genes_genome.pdf': {}}]], 'breakpoints_html': [[{'meta': {}}, {'*/*_genome_copynumbers_breakpoints.html': {}}]], 'breakpoints_pdf': [[{'meta': {}}, {'*/*_genome_copynumbers_breakpoints.pdf': {}}]], 'breakpoints_subclonal_html': [[{'meta': {}}, {'*/*_genome_copynumbers_breakpoints_subclonal.html': {}}]], 'breakpoints_subclonal_pdf': [[{'meta': {}}, {'*/*_genome_copynumbers_breakpoints_subclonal.pdf': {}}]], 'copynumbers_details_html': [[{'meta': {}}, {'*/*_genome_copynumbers_details.html': {}}]], 'copynumbers_details_pdf': [[{'meta': {}}, {'*/*_genome_copynumbers_details.pdf': {}}]], 'bed_files': [[{'meta': {}}, {'*/bed_output/*.bed': {}}]], 'variation_plots': [[{'meta': {}}, {'*/variation_plots/*.html': {}}]], 'vcf_files': [[{'meta': {}}, {'*/vcf_output/*_wakhan_cna_*.vcf': {}}]], 'heatmap_html': [[{'meta': {}}, {'*_heatmap_ploidy_purity.html': {}}]], 'heatmap_pdf': [[{'meta': {}}, {'*_heatmap_ploidy_purity.html.pdf': {}}]], 'optimized_peak_html': [[{'meta': {}}, {'*_optimized_peak.html': {}}]], 'coverage_csv': [[{'meta': {}}, {'coverage_data/*.csv': {}}]], 'coverage_plots_html': [[{'meta': {}}, {'coverage_plots/*.html': {}}]], 'coverage_plots_pdf': [[{'meta': {}}, {'coverage_plots/*.pdf': {}}]], 'phasing_html': [[{'meta': {}}, {'phasing_output/*.html': {}}]], 'phasing_pdf': [[{'meta': {}}, {'phasing_output/*.pdf': {}}]], 'rephased_vcf': [[{'meta': {}}, {'phasing_output/*.rephased.vcf.gz': {}}]], 'rephased_vcf_index': [[{'meta': {}}, {'phasing_output/*.rephased.vcf.gz.csi': {}}]], 'snps_loh_plot': [[{'meta': {}}, {'snps_loh_plots/*_genome_snps_ratio_loh.html': {}}]], 'solutions_ranks': [[{'meta': {}}, {'solutions_ranks.tsv': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*/*_genes_genome.html") , emit: genes_genome_html - tuple val(meta), path("*/*_genes_genome.pdf") , emit: genes_genome_pdf - tuple val(meta), path("*/*_genome_copynumbers_breakpoints.html") , emit: breakpoints_html - tuple val(meta), path("*/*_genome_copynumbers_breakpoints.pdf") , emit: breakpoints_pdf - tuple val(meta), path("*/*_genome_copynumbers_breakpoints_subclonal.html") , emit: breakpoints_subclonal_html - tuple val(meta), path("*/*_genome_copynumbers_breakpoints_subclonal.pdf") , emit: breakpoints_subclonal_pdf - tuple val(meta), path("*/*_genome_copynumbers_details.html") , emit: copynumbers_details_html - tuple val(meta), path("*/*_genome_copynumbers_details.pdf") , emit: copynumbers_details_pdf - tuple val(meta), path("*/bed_output/*.bed") , emit: bed_files - tuple val(meta), path("*/variation_plots/*.html") , emit: variation_plots - tuple val(meta), path("*/vcf_output/*_wakhan_cna_*.vcf") , emit: vcf_files - tuple val(meta), path("*_heatmap_ploidy_purity.html") , emit: heatmap_html - tuple val(meta), path("*_heatmap_ploidy_purity.html.pdf") , emit: heatmap_pdf - tuple val(meta), path("*_optimized_peak.html") , emit: optimized_peak_html - tuple val(meta), path("coverage_data/*.csv") , emit: coverage_csv - tuple val(meta), path("coverage_plots/*.html") , emit: coverage_plots_html - tuple val(meta), path("coverage_plots/*.pdf") , emit: coverage_plots_pdf - tuple val(meta), path("phasing_output/*.html") , emit: phasing_html - tuple val(meta), path("phasing_output/*.pdf") , emit: phasing_pdf - tuple val(meta), path("phasing_output/*.rephased.vcf.gz") , emit: rephased_vcf - tuple val(meta), path("phasing_output/*.rephased.vcf.gz.csi") , emit: rephased_vcf_index - tuple val(meta), path("snps_loh_plots/*_genome_snps_ratio_loh.html") , emit: snps_loh_plot, optional: true - tuple val(meta), path("solutions_ranks.tsv") , emit: solutions_ranks - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/wakhan/main.nf -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found 3 inputs in modules/local/clairs/main.nf -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'tumor_bam': {}}, {'tumor_bai': {}}, {'normal_bam': {}}, {'normal_bai': {}}, {'model': {}}], [{'meta2': {}}, {'reference': {}}], [{'meta3': {}}, {'index': {}}]] -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.vcf.gz"), emit: vcfs - tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi - path "versions.yml", emit: versions - - -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found 3 outputs in modules/local/clairs/main.nf -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcfs': [[{'meta': {}}, {'*.vcf.gz': {}}]], 'tbi': [[{'meta': {}}, {'*.vcf.gz.tbi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.vcf.gz"), emit: vcfs - tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi - path "versions.yml", emit: versions - - -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/clairs/main.nf -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/cramino/main.nf -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}]] -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.txt"), emit: txt - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/local/cramino/main.nf -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Outputs: {'txt': [[{'meta': {}}, {'*.txt': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.txt"), emit: txt - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/cramino/main.nf -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/metaextract/main.nf -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}]] -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), env(basecall_model), env(kinetics) , emit: meta_ext - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/local/metaextract/main.nf -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Outputs: {'meta_ext': [[{'meta': {}}, {'basecall_model': {}}, {'kinetics': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), env(basecall_model), env(kinetics) , emit: meta_ext - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/metaextract/main.nf -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 7 inputs in modules/local/clairsto/main.nf -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'tumor_bam': {}}, {'tumor_bai': {}}, {'model': {}}], [{'meta2': {}}, {'reference': {}}], [{'meta3': {}}, {'index': {}}], {'dbSNP': {}}, {'colors': {}}, {'onekgenomes': {}}, {'gnomad': {}}] -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("indel.vcf.gz"), emit: indel_vcf - tuple val(meta), path("indel.vcf.gz.tbi"), emit: indel_tbi - tuple val(meta), path("snv.vcf.gz"), emit: snv_vcf - tuple val(meta), path("snv.vcf.gz.tbi"), emit: snv_tbi - path "versions.yml", emit: versions - - -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 5 outputs in modules/local/clairsto/main.nf -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Outputs: {'indel_vcf': [[{'meta': {}}, {'indel.vcf.gz': {}}]], 'indel_tbi': [[{'meta': {}}, {'indel.vcf.gz.tbi': {}}]], 'snv_vcf': [[{'meta': {}}, {'snv.vcf.gz': {}}]], 'snv_tbi': [[{'meta': {}}, {'snv.vcf.gz.tbi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("indel.vcf.gz"), emit: indel_vcf - tuple val(meta), path("indel.vcf.gz.tbi"), emit: indel_tbi - tuple val(meta), path("snv.vcf.gz"), emit: snv_vcf - tuple val(meta), path("snv.vcf.gz.tbi"), emit: snv_tbi - path "versions.yml", emit: versions - - -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/clairsto/main.nf -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/fibertoolsrs/fire/main.nf -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}]] -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found output_data: - // TODO nf-core: Named file extensions MUST be emitted for ALL output channels - tuple val(meta), path("*.bam"), emit: bam - // TODO nf-core: List additional required output channels/values here - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/local/fibertoolsrs/fire/main.nf -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bam': [[{'meta': {}}, {'*.bam': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Output data: - // TODO nf-core: Named file extensions MUST be emitted for ALL output channels - tuple val(meta), path("*.bam"), emit: bam - // TODO nf-core: List additional required output channels/values here - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/fibertoolsrs/fire/main.nf -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/fibertoolsrs/predictm6a/main.nf -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}]] -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found output_data: - // TODO nf-core: Named file extensions MUST be emitted for ALL output channels - tuple val(meta), path("*.bam"), emit: bam - // TODO nf-core: List additional required output channels/values here - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/local/fibertoolsrs/predictm6a/main.nf -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bam': [[{'meta': {}}, {'*.bam': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Output data: - // TODO nf-core: Named file extensions MUST be emitted for ALL output channels - tuple val(meta), path("*.bam"), emit: bam - // TODO nf-core: List additional required output channels/values here - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/fibertoolsrs/predictm6a/main.nf -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/fibertoolsrs/qc/main.nf -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}]] -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found output_data: - // TODO nf-core: Named file extensions MUST be emitted for ALL output channels - tuple val(meta), path("*.txt"), emit: qc_txt - // TODO nf-core: List additional required output channels/values here - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/local/fibertoolsrs/qc/main.nf -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Outputs: {'qc_txt': [[{'meta': {}}, {'*.txt': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Output data: - // TODO nf-core: Named file extensions MUST be emitted for ALL output channels - tuple val(meta), path("*.txt"), emit: qc_txt - // TODO nf-core: List additional required output channels/values here - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/fibertoolsrs/qc/main.nf -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/fibertoolsrs/nucleosomes/main.nf -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}]] -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found output_data: - // TODO nf-core: Named file extensions MUST be emitted for ALL output channels - tuple val(meta), path("*.bam"), emit: bam - // TODO nf-core: List additional required output channels/values here - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/local/fibertoolsrs/nucleosomes/main.nf -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bam': [[{'meta': {}}, {'*.bam': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Output data: - // TODO nf-core: Named file extensions MUST be emitted for ALL output channels - tuple val(meta), path("*.bam"), emit: bam - // TODO nf-core: List additional required output channels/values here - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/fibertoolsrs/nucleosomes/main.nf -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/vcfsplit/main.nf -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'snv_vcf': {}}, {'indel_vcf': {}}]] -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*somatic.vcf.gz") , emit: somatic_vcf - tuple val(meta), path("*somatic.vcf.gz.tbi") , emit: somatic_tbi - tuple val(meta), path("*germline.vcf.gz") , emit: germline_vcf - tuple val(meta), path("*germline.vcf.gz.tbi") , emit: germline_tbi - - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 5 outputs in modules/local/vcfsplit/main.nf -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Outputs: {'somatic_vcf': [[{'meta': {}}, {'*somatic.vcf.gz': {}}]], 'somatic_tbi': [[{'meta': {}}, {'*somatic.vcf.gz.tbi': {}}]], 'germline_vcf': [[{'meta': {}}, {'*germline.vcf.gz': {}}]], 'germline_tbi': [[{'meta': {}}, {'*germline.vcf.gz.tbi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*somatic.vcf.gz") , emit: somatic_vcf - tuple val(meta), path("*somatic.vcf.gz.tbi") , emit: somatic_tbi - tuple val(meta), path("*germline.vcf.gz") , emit: germline_vcf - tuple val(meta), path("*germline.vcf.gz.tbi") , emit: germline_tbi - - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/vcfsplit/main.nf -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 3 inputs in modules/local/clair3/main.nf -[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}, {'model': {}}, {'platform': {}}], [{'meta2': {}}, {'reference': {}}], [{'meta3': {}}, {'index': {}}]] -[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*merge_output.vcf.gz"), emit: vcf - tuple val(meta), path("*merge_output.vcf.gz.tbi"), emit: tbi - tuple val(meta), path("*phased_merge_output.vcf.gz"), emit: phased_vcf, optional: true - tuple val(meta), path("*phased_merge_output.vcf.gz.tbi"), emit: phased_tbi, optional: true - path "versions.yml", emit: versions - - -[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Found 5 outputs in modules/local/clair3/main.nf -[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcf': [[{'meta': {}}, {'*merge_output.vcf.gz': {}}]], 'tbi': [[{'meta': {}}, {'*merge_output.vcf.gz.tbi': {}}]], 'phased_vcf': [[{'meta': {}}, {'*phased_merge_output.vcf.gz': {}}]], 'phased_tbi': [[{'meta': {}}, {'*phased_merge_output.vcf.gz.tbi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*merge_output.vcf.gz"), emit: vcf - tuple val(meta), path("*merge_output.vcf.gz.tbi"), emit: tbi - tuple val(meta), path("*phased_merge_output.vcf.gz"), emit: phased_vcf, optional: true - tuple val(meta), path("*phased_merge_output.vcf.gz.tbi"), emit: phased_tbi, optional: true - path "versions.yml", emit: versions - - -[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/clair3/main.nf -[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Found 8 inputs in modules/nf-core/ascat/main.nf -[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'input_normal': {}}, {'index_normal': {}}, {'input_tumor': {}}, {'index_tumor': {}}], {'genomeVersion': {}}, {'allele_files': {}}, {'loci_files': {}}, {'bed_file': {}}, {'fasta': {}}, {'gc_file': {}}, {'rt_file': {}}] -[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*alleleFrequencies_chr*.txt"), emit: allelefreqs - tuple val(meta), path("*BAF.txt"), emit: bafs - tuple val(meta), path("*cnvs.txt"), emit: cnvs - tuple val(meta), path("*LogR.txt"), emit: logrs - tuple val(meta), path("*metrics.txt"), emit: metrics - tuple val(meta), path("*png"), emit: png - tuple val(meta), path("*pdf"), emit: pdf, optional: true - tuple val(meta), path("*purityploidy.txt"), emit: purityploidy - tuple val(meta), path("*segments.txt"), emit: segments - tuple val(meta), path("*segments_raw.txt"), emit: segments_raw, optional: true - path "versions.yml", emit: versions - - -[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Found 11 outputs in modules/nf-core/ascat/main.nf -[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Outputs: {'allelefreqs': [[{'meta': {}}, {'*alleleFrequencies_chr*.txt': {}}]], 'bafs': [[{'meta': {}}, {'*BAF.txt': {}}]], 'cnvs': [[{'meta': {}}, {'*cnvs.txt': {}}]], 'logrs': [[{'meta': {}}, {'*LogR.txt': {}}]], 'metrics': [[{'meta': {}}, {'*metrics.txt': {}}]], 'png': [[{'meta': {}}, {'*png': {}}]], 'pdf': [[{'meta': {}}, {'*pdf': {}}]], 'purityploidy': [[{'meta': {}}, {'*purityploidy.txt': {}}]], 'segments': [[{'meta': {}}, {'*segments.txt': {}}]], 'segments_raw': [[{'meta': {}}, {'*segments_raw.txt': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*alleleFrequencies_chr*.txt"), emit: allelefreqs - tuple val(meta), path("*BAF.txt"), emit: bafs - tuple val(meta), path("*cnvs.txt"), emit: cnvs - tuple val(meta), path("*LogR.txt"), emit: logrs - tuple val(meta), path("*metrics.txt"), emit: metrics - tuple val(meta), path("*png"), emit: png - tuple val(meta), path("*pdf"), emit: pdf, optional: true - tuple val(meta), path("*purityploidy.txt"), emit: purityploidy - tuple val(meta), path("*segments.txt"), emit: segments - tuple val(meta), path("*segments_raw.txt"), emit: segments_raw, optional: true - path "versions.yml", emit: versions - - -[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/ascat/main.nf -[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:36,574] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:50:36,575] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:36,839] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:36,851] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:50:36,851] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:50:36,852] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:50:36,852] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:36,884] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:36,887] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/ascat'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:36,888] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/ascat'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:36,986] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:37,056] nf_core.components.components_differ [DEBUG ] Applying patch to modules/nf-core/ascat/main.nf -[2025-11-27 15:50:37,056] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/bcftools/concat/main.nf -[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'vcfs': {}}, {'tbi': {}}]] -[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("${prefix}.${extension}") , emit: vcf - tuple val(meta), path("${prefix}.${extension}.tbi"), emit: tbi, optional: true - tuple val(meta), path("${prefix}.${extension}.csi"), emit: csi, optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Found 4 outputs in modules/nf-core/bcftools/concat/main.nf -[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcf': [[{'meta': {}}, {'${prefix}.${extension}': {}}]], 'tbi': [[{'meta': {}}, {'${prefix}.${extension}.tbi': {}}]], 'csi': [[{'meta': {}}, {'${prefix}.${extension}.csi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("${prefix}.${extension}") , emit: vcf - tuple val(meta), path("${prefix}.${extension}.tbi"), emit: tbi, optional: true - tuple val(meta), path("${prefix}.${extension}.csi"), emit: csi, optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/bcftools/concat/main.nf -[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:37,057] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:50:37,058] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:37,092] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:37,103] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:50:37,103] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:50:37,103] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:50:37,104] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:37,135] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:37,138] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/bcftools/concat'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:37,139] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/bcftools/concat'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:37,225] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:37,309] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:50:37,310] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:37,343] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:37,353] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:50:37,354] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:50:37,354] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:50:37,354] git.cmd [DEBUG ] Popen(['git', 'checkout', 'e753770db613ce014b3c4bc94f6cba443427b726'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:38,018] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:38,212] nf_core.components.nfcore_component [DEBUG ] Found 4 inputs in modules/nf-core/bcftools/merge/main.nf -[2025-11-27 15:50:38,212] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'vcfs': {}}, {'tbis': {}}], [{'meta2': {}}, {'fasta': {}}], [{'meta3': {}}, {'fai': {}}], [{'meta4': {}}, {'bed': {}}]] -[2025-11-27 15:50:38,212] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.{bcf,vcf}{,.gz}"), emit: vcf - tuple val(meta), path("*.{csi,tbi}") , emit: index, optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:38,212] nf_core.components.nfcore_component [DEBUG ] Found 3 outputs in modules/nf-core/bcftools/merge/main.nf -[2025-11-27 15:50:38,213] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcf': [[{'meta': {}}, {'*.{bcf,vcf}{,.gz}': {}}]], 'index': [[{'meta': {}}, {'*.{csi,tbi}': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:38,213] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.{bcf,vcf}{,.gz}"), emit: vcf - tuple val(meta), path("*.{csi,tbi}") , emit: index, optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:38,213] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/bcftools/merge/main.nf -[2025-11-27 15:50:38,213] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:38,213] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:50:38,213] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:38,275] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:38,286] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:50:38,287] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:50:38,287] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:50:38,288] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:38,346] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:38,350] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/bcftools/merge'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:38,351] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/bcftools/merge'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:38,436] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:38,518] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:50:38,518] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:38,566] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:38,578] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:50:38,578] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:50:38,578] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:50:38,579] git.cmd [DEBUG ] Popen(['git', 'checkout', 'f17049e03697726ace7499d2fe342f892594f6f3'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:42,382] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/bcftools/sort/main.nf -[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'vcf': {}}]] -[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf - tuple val(meta), path("*.tbi") , emit: tbi, optional: true - tuple val(meta), path("*.csi") , emit: csi, optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Found 4 outputs in modules/nf-core/bcftools/sort/main.nf -[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcf': [[{'meta': {}}, {'*.{vcf,vcf.gz,bcf,bcf.gz}': {}}]], 'tbi': [[{'meta': {}}, {'*.tbi': {}}]], 'csi': [[{'meta': {}}, {'*.csi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf - tuple val(meta), path("*.tbi") , emit: tbi, optional: true - tuple val(meta), path("*.csi") , emit: csi, optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/bcftools/sort/main.nf -[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:45,573] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:50:45,574] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:45,713] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:45,727] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:50:45,727] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:50:45,727] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:50:45,728] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:45,865] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:45,868] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/bcftools/sort'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:45,869] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/bcftools/sort'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:45,959] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:46,043] nf_core.components.components_differ [DEBUG ] Applying patch to modules/nf-core/bcftools/sort/main.nf -[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/ensemblvep/download/main.nf -[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'assembly': {}}, {'species': {}}, {'cache_version': {}}]] -[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path(prefix), emit: cache - path "versions.yml", emit: versions - - -[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/ensemblvep/download/main.nf -[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Outputs: {'cache': [[{'meta': {}}, {'prefix': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path(prefix), emit: cache - path "versions.yml", emit: versions - - -[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/ensemblvep/download/main.nf -[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:46,044] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:50:46,045] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:46,151] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:46,164] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:50:46,164] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:50:46,164] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:50:46,165] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:46,208] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:46,212] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/ensemblvep/download'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:46,213] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/ensemblvep/download'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:46,324] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:46,402] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:50:46,402] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:46,455] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:46,467] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:50:46,467] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:50:46,467] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:50:46,468] git.cmd [DEBUG ] Popen(['git', 'checkout', '2fcc53751152a999bfc9c24f75f494b9e5bb338f'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:49,974] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Found 9 inputs in modules/nf-core/ensemblvep/vep/main.nf -[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'vcf': {}}, {'custom_extra_files': {}}], {'genome': {}}, {'species': {}}, {'cache_version': {}}, {'cache': {}}, [{'meta2': {}}, {'fasta': {}}], {'extra_files': {}}, {'custom_vep': {}}, {'custom_vep_tbi': {}}] -[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.vcf.gz"), emit: vcf, optional: true - tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi, optional: true - tuple val(meta), path("*.tab.gz"), emit: tab, optional: true - tuple val(meta), path("*.json.gz"), emit: json, optional: true - path "*.html", emit: report, optional: true - path "versions.yml", emit: versions - - -[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Found 6 outputs in modules/nf-core/ensemblvep/vep/main.nf -[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcf': [[{'meta': {}}, {'*.vcf.gz': {}}]], 'tbi': [[{'meta': {}}, {'*.vcf.gz.tbi': {}}]], 'tab': [[{'meta': {}}, {'*.tab.gz': {}}]], 'json': [[{'meta': {}}, {'*.json.gz': {}}]], 'report': [{'*.html': {}}], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.vcf.gz"), emit: vcf, optional: true - tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi, optional: true - tuple val(meta), path("*.tab.gz"), emit: tab, optional: true - tuple val(meta), path("*.json.gz"), emit: json, optional: true - path "*.html", emit: report, optional: true - path "versions.yml", emit: versions - - -[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/ensemblvep/vep/main.nf -[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:53,302] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:50:53,303] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,408] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,420] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:50:53,420] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:50:53,420] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:50:53,421] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,518] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,522] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/ensemblvep/vep'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,523] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/ensemblvep/vep'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,631] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,709] nf_core.components.components_differ [DEBUG ] Applying patch to modules/nf-core/ensemblvep/vep/main.nf -[2025-11-27 15:50:53,709] nf_core.components.nfcore_component [DEBUG ] Found 3 inputs in modules/nf-core/longphase/haplotag/main.nf -[2025-11-27 15:50:53,709] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}, {'snps': {}}, {'svs': {}}, {'mods': {}}], [{'meta2': {}}, {'fasta': {}}], [{'meta3': {}}, {'fai': {}}]] -[2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.{bam,cram}"), emit: bam - tuple val(meta), path("*.log") , emit: log , optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Found 3 outputs in modules/nf-core/longphase/haplotag/main.nf -[2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bam': [[{'meta': {}}, {'*.{bam,cram}': {}}]], 'log': [[{'meta': {}}, {'*.log': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.{bam,cram}"), emit: bam - tuple val(meta), path("*.log") , emit: log , optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/longphase/haplotag/main.nf -[2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:50:53,710] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:50:53,711] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,792] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,804] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:50:53,805] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:50:53,806] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:50:53,806] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,874] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,878] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/longphase/haplotag'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,879] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/longphase/haplotag'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:53,991] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:50:54,094] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:50:54,095] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:54,185] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:54,199] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:50:54,199] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:50:54,200] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:50:54,200] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:50:58,312] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Found 3 inputs in modules/nf-core/longphase/phase/main.nf -[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}, {'snps': {}}, {'svs': {}}, {'mods': {}}], [{'meta2': {}}, {'fasta': {}}], [{'meta3': {}}, {'fai': {}}]] -[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.vcf.gz") , emit: vcf - tuple val(meta), path("*.vcf.gz.tbi") , emit: tbi - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Found 3 outputs in modules/nf-core/longphase/phase/main.nf -[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcf': [[{'meta': {}}, {'*.vcf.gz': {}}]], 'tbi': [[{'meta': {}}, {'*.vcf.gz.tbi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.vcf.gz") , emit: vcf - tuple val(meta), path("*.vcf.gz.tbi") , emit: tbi - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/longphase/phase/main.nf -[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:51:02,039] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:02,040] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:02,408] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:02,419] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:02,419] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:02,420] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:02,421] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:02,475] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:02,478] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/longphase/phase'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:02,479] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/longphase/phase'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:02,590] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:02,695] nf_core.components.components_differ [DEBUG ] Applying patch to modules/nf-core/longphase/phase/main.nf -[2025-11-27 15:51:02,695] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:02,696] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:02,749] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:02,761] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:02,761] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:02,761] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:02,762] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:05,703] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Found 6 inputs in modules/nf-core/minimap2/align/main.nf -[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'reads': {}}], [{'meta2': {}}, {'reference': {}}], {'bam_format': {}}, {'bam_index_extension': {}}, {'cigar_paf_format': {}}, {'cigar_bam': {}}] -[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.paf") , optional: true, emit: paf - tuple val(meta), path("*.bam") , optional: true, emit: bam - tuple val(meta), path("*.bam.${bam_index_extension}"), optional: true, emit: index - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Found 4 outputs in modules/nf-core/minimap2/align/main.nf -[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Outputs: {'paf': [[{'meta': {}}, {'*.paf': {}}]], 'bam': [[{'meta': {}}, {'*.bam': {}}]], 'index': [[{'meta': {}}, {'*.bam.${bam_index_extension}': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.paf") , optional: true, emit: paf - tuple val(meta), path("*.bam") , optional: true, emit: bam - tuple val(meta), path("*.bam.${bam_index_extension}"), optional: true, emit: index - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/minimap2/align/main.nf -[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:51:09,496] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:09,497] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:09,655] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:09,667] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:09,667] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:09,667] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:09,668] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:09,808] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:09,812] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/minimap2/align'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:09,813] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/minimap2/align'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:09,901] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:10,040] nf_core.components.components_differ [DEBUG ] Applying patch to modules/nf-core/minimap2/align/main.nf -[2025-11-27 15:51:10,041] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:10,041] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:10,141] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:10,153] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:10,153] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:10,154] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:10,154] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:13,177] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/minimap2/index/main.nf -[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'fasta': {}}]] -[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.mmi"), emit: index - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/minimap2/index/main.nf -[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Outputs: {'index': [[{'meta': {}}, {'*.mmi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.mmi"), emit: index - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/minimap2/index/main.nf -[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:51:16,904] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:16,905] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:17,209] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:17,221] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:17,221] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:17,222] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:17,222] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:17,280] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:17,284] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/minimap2/index'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:17,285] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/minimap2/index'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:17,372] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:17,510] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:17,510] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:17,570] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:17,582] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:17,583] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:17,583] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:17,583] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:20,761] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:24,622] nf_core.components.nfcore_component [DEBUG ] Found 3 inputs in modules/nf-core/modkit/pileup/main.nf -[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}], [{'meta2': {}}, {'fasta': {}}, {'fai': {}}], [{'meta3': {}}, {'bed': {}}]] -[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.bed") , emit: bed , optional: true - tuple val(meta), path("*.bedgraph"), emit: bedgraph, optional: true - tuple val(meta), path("*.log") , emit: log , optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Found 4 outputs in modules/nf-core/modkit/pileup/main.nf -[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bed': [[{'meta': {}}, {'*.bed': {}}]], 'bedgraph': [[{'meta': {}}, {'*.bedgraph': {}}]], 'log': [[{'meta': {}}, {'*.log': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.bed") , emit: bed , optional: true - tuple val(meta), path("*.bedgraph"), emit: bedgraph, optional: true - tuple val(meta), path("*.log") , emit: log , optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/modkit/pileup/main.nf -[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:51:24,623] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:24,624] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:24,815] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:24,826] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:24,827] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:24,827] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:24,828] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:24,997] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:25,000] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/modkit/pileup'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:25,002] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/modkit/pileup'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:25,119] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:25,234] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:25,235] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:25,374] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:25,386] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:25,386] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:25,386] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:25,387] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:28,381] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:32,189] nf_core.components.nfcore_component [DEBUG ] Found 2 inputs in modules/nf-core/mosdepth/main.nf -[2025-11-27 15:51:32,189] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}, {'bed': {}}], [{'meta2': {}}, {'fasta': {}}]] -[2025-11-27 15:51:32,189] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path('*.global.dist.txt') , emit: global_txt - tuple val(meta), path('*.summary.txt') , emit: summary_txt - tuple val(meta), path('*.region.dist.txt') , optional:true, emit: regions_txt - tuple val(meta), path('*.per-base.d4') , optional:true, emit: per_base_d4 - tuple val(meta), path('*.per-base.bed.gz') , optional:true, emit: per_base_bed - tuple val(meta), path('*.per-base.bed.gz.csi') , optional:true, emit: per_base_csi - tuple val(meta), path('*.regions.bed.gz') , optional:true, emit: regions_bed - tuple val(meta), path('*.regions.bed.gz.csi') , optional:true, emit: regions_csi - tuple val(meta), path('*.quantized.bed.gz') , optional:true, emit: quantized_bed - tuple val(meta), path('*.quantized.bed.gz.csi') , optional:true, emit: quantized_csi - tuple val(meta), path('*.thresholds.bed.gz') , optional:true, emit: thresholds_bed - tuple val(meta), path('*.thresholds.bed.gz.csi'), optional:true, emit: thresholds_csi - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:32,190] nf_core.components.nfcore_component [DEBUG ] Found 13 outputs in modules/nf-core/mosdepth/main.nf -[2025-11-27 15:51:32,190] nf_core.components.nfcore_component [DEBUG ] Outputs: {'global_txt': [[{'meta': {}}, {'*.global.dist.txt': {}}]], 'summary_txt': [[{'meta': {}}, {'*.summary.txt': {}}]], 'regions_txt': [[{'meta': {}}, {'*.region.dist.txt': {}}]], 'per_base_d4': [[{'meta': {}}, {'*.per-base.d4': {}}]], 'per_base_bed': [[{'meta': {}}, {'*.per-base.bed.gz': {}}]], 'per_base_csi': [[{'meta': {}}, {'*.per-base.bed.gz.csi': {}}]], 'regions_bed': [[{'meta': {}}, {'*.regions.bed.gz': {}}]], 'regions_csi': [[{'meta': {}}, {'*.regions.bed.gz.csi': {}}]], 'quantized_bed': [[{'meta': {}}, {'*.quantized.bed.gz': {}}]], 'quantized_csi': [[{'meta': {}}, {'*.quantized.bed.gz.csi': {}}]], 'thresholds_bed': [[{'meta': {}}, {'*.thresholds.bed.gz': {}}]], 'thresholds_csi': [[{'meta': {}}, {'*.thresholds.bed.gz.csi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:51:32,190] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path('*.global.dist.txt') , emit: global_txt - tuple val(meta), path('*.summary.txt') , emit: summary_txt - tuple val(meta), path('*.region.dist.txt') , optional:true, emit: regions_txt - tuple val(meta), path('*.per-base.d4') , optional:true, emit: per_base_d4 - tuple val(meta), path('*.per-base.bed.gz') , optional:true, emit: per_base_bed - tuple val(meta), path('*.per-base.bed.gz.csi') , optional:true, emit: per_base_csi - tuple val(meta), path('*.regions.bed.gz') , optional:true, emit: regions_bed - tuple val(meta), path('*.regions.bed.gz.csi') , optional:true, emit: regions_csi - tuple val(meta), path('*.quantized.bed.gz') , optional:true, emit: quantized_bed - tuple val(meta), path('*.quantized.bed.gz.csi') , optional:true, emit: quantized_csi - tuple val(meta), path('*.thresholds.bed.gz') , optional:true, emit: thresholds_bed - tuple val(meta), path('*.thresholds.bed.gz.csi'), optional:true, emit: thresholds_csi - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:32,190] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/mosdepth/main.nf -[2025-11-27 15:51:32,190] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:51:32,190] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:32,191] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:32,284] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:32,295] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:32,296] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:32,297] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:32,298] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:32,363] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:32,367] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/mosdepth'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:32,368] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/mosdepth'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:32,456] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:32,599] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:32,600] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:32,663] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:32,674] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:32,675] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:32,675] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:32,675] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:35,682] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Found 6 inputs in modules/nf-core/multiqc/main.nf -[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Inputs: [{'multiqc_files': {}}, {'multiqc_config': {}}, {'extra_multiqc_config': {}}, {'multiqc_logo': {}}, {'replace_names': {}}, {'sample_names': {}}] -[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Found output_data: - path "*multiqc_report.html", emit: report - path "*_data" , emit: data - path "*_plots" , optional:true, emit: plots - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Found 4 outputs in modules/nf-core/multiqc/main.nf -[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Outputs: {'report': [{'*multiqc_report.html': {}}], 'data': [{'*_data': {}}], 'plots': [{'*_plots': {}}], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Output data: - path "*multiqc_report.html", emit: report - path "*_data" , emit: data - path "*_plots" , optional:true, emit: plots - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/multiqc/main.nf -[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:51:39,445] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:39,446] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:39,663] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:39,675] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:39,675] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:39,676] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:39,677] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:39,806] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:39,810] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/multiqc'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:39,811] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/multiqc'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:39,903] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:40,049] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:40,050] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:40,147] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:40,160] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:40,160] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:40,161] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:40,161] git.cmd [DEBUG ] Popen(['git', 'checkout', 'a4488d3d09244f29fb4606ba4eef85d59dcc6ad8'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:43,079] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:46,118] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/pigz/uncompress/main.nf -[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'zip': {}}]] -[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("${uncompressed_filename}") , emit: file - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/pigz/uncompress/main.nf -[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Outputs: {'file': [[{'meta': {}}, {'${uncompressed_filename}': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("${uncompressed_filename}") , emit: file - path "versions.yml" , emit: versions - - -[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/pigz/uncompress/main.nf -[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:51:46,119] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:46,120] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:46,170] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:46,183] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:46,184] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:46,184] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:46,185] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:46,235] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:46,239] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/pigz/uncompress'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:46,240] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/pigz/uncompress'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:46,362] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:46,485] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:46,486] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:46,557] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:46,569] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:46,569] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:46,569] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:46,570] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:49,638] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/samtools/cat/main.nf -[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'input_files': {}}]] -[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam - tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram - path "versions.yml" , emit: versions - - - -[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Found 3 outputs in modules/nf-core/samtools/cat/main.nf -[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bam': [[{'meta': {}}, {'${prefix}.bam': {}}]], 'cram': [[{'meta': {}}, {'${prefix}.cram': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam - tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram - path "versions.yml" , emit: versions - - - -[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/samtools/cat/main.nf -[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:51:53,446] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:53,447] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:53,665] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:53,676] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:53,676] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:53,677] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:53,678] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:53,816] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:53,820] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/samtools/cat'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:53,821] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/samtools/cat'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:53,937] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:51:54,075] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:51:54,076] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:54,183] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:54,194] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:51:54,195] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:51:54,195] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:51:54,195] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:51:57,097] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Found 3 inputs in modules/nf-core/samtools/faidx/main.nf -[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'fasta': {}}], [{'meta2': {}}, {'fai': {}}], {'get_sizes': {}}] -[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path ("*.{fa,fasta}") , emit: fa, optional: true - tuple val(meta), path ("*.sizes") , emit: sizes, optional: true - tuple val(meta), path ("*.fai") , emit: fai, optional: true - tuple val(meta), path ("*.gzi") , emit: gzi, optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Found 5 outputs in modules/nf-core/samtools/faidx/main.nf -[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Outputs: {'fa': [[{'meta': {}}, {'*.{fa,fasta}': {}}]], 'sizes': [[{'meta': {}}, {'*.sizes': {}}]], 'fai': [[{'meta': {}}, {'*.fai': {}}]], 'gzi': [[{'meta': {}}, {'*.gzi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path ("*.{fa,fasta}") , emit: fa, optional: true - tuple val(meta), path ("*.sizes") , emit: sizes, optional: true - tuple val(meta), path ("*.fai") , emit: fai, optional: true - tuple val(meta), path ("*.gzi") , emit: gzi, optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/samtools/faidx/main.nf -[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:52:00,645] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:00,646] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:00,838] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:00,851] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:00,851] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:00,851] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:00,852] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:01,041] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:01,045] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/samtools/faidx'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:01,046] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/samtools/faidx'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:01,137] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:01,305] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:01,306] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:01,372] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:01,385] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:01,385] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:01,386] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:01,386] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:04,805] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/samtools/flagstat/main.nf -[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}]] -[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.flagstat"), emit: flagstat - path "versions.yml" , emit: versions - - -[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/samtools/flagstat/main.nf -[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Outputs: {'flagstat': [[{'meta': {}}, {'*.flagstat': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.flagstat"), emit: flagstat - path "versions.yml" , emit: versions - - -[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/samtools/flagstat/main.nf -[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:52:08,779] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:08,780] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:09,027] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:09,038] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:09,038] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:09,039] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:09,040] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:09,096] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:09,100] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/samtools/flagstat'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:09,101] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/samtools/flagstat'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:09,188] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:09,355] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:09,356] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:09,413] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:09,426] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:09,426] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:09,426] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:09,426] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:12,547] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:16,622] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/samtools/idxstats/main.nf -[2025-11-27 15:52:16,622] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}]] -[2025-11-27 15:52:16,622] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.idxstats"), emit: idxstats - path "versions.yml" , emit: versions - - -[2025-11-27 15:52:16,623] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/samtools/idxstats/main.nf -[2025-11-27 15:52:16,623] nf_core.components.nfcore_component [DEBUG ] Outputs: {'idxstats': [[{'meta': {}}, {'*.idxstats': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:52:16,623] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.idxstats"), emit: idxstats - path "versions.yml" , emit: versions - - -[2025-11-27 15:52:16,623] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/samtools/idxstats/main.nf -[2025-11-27 15:52:16,623] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:52:16,623] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:16,623] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:16,766] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:16,778] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:16,778] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:16,779] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:16,779] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:16,892] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:16,896] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/samtools/idxstats'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:16,897] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/samtools/idxstats'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:16,985] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:17,153] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:17,154] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:17,256] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:17,268] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:17,268] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:17,269] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:17,269] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:20,320] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/samtools/index/main.nf -[2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'input': {}}]] -[2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.bai") , optional:true, emit: bai - tuple val(meta), path("*.csi") , optional:true, emit: csi - tuple val(meta), path("*.crai"), optional:true, emit: crai - path "versions.yml" , emit: versions - - -[2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Found 4 outputs in modules/nf-core/samtools/index/main.nf -[2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bai': [[{'meta': {}}, {'*.bai': {}}]], 'csi': [[{'meta': {}}, {'*.csi': {}}]], 'crai': [[{'meta': {}}, {'*.crai': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.bai") , optional:true, emit: bai - tuple val(meta), path("*.csi") , optional:true, emit: csi - tuple val(meta), path("*.crai"), optional:true, emit: crai - path "versions.yml" , emit: versions - - -[2025-11-27 15:52:23,974] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/samtools/index/main.nf -[2025-11-27 15:52:23,974] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:52:23,974] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:23,974] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:24,244] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:24,256] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:24,256] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:24,257] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:24,257] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:24,308] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:24,312] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/samtools/index'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:24,313] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/samtools/index'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:24,401] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:24,568] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:24,569] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:24,620] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:24,631] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:24,632] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:24,632] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:24,632] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:27,563] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Found 2 inputs in modules/nf-core/samtools/stats/main.nf -[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'input': {}}, {'input_index': {}}], [{'meta2': {}}, {'fasta': {}}]] -[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("*.stats"), emit: stats - path "versions.yml" , emit: versions - - -[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/samtools/stats/main.nf -[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Outputs: {'stats': [[{'meta': {}}, {'*.stats': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("*.stats"), emit: stats - path "versions.yml" , emit: versions - - -[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/samtools/stats/main.nf -[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:52:31,361] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:31,362] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:31,494] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:31,506] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:31,507] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:31,507] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:31,508] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:31,610] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:31,614] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/samtools/stats'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:31,615] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/samtools/stats'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:31,702] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:31,878] nf_core.components.components_differ [DEBUG ] Applying patch to modules/nf-core/samtools/stats/main.nf -[2025-11-27 15:52:31,878] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:31,879] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:31,963] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:31,975] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:31,976] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:31,976] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:31,976] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:34,930] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Found 2 inputs in modules/nf-core/severus/main.nf -[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'target_input': {}}, {'target_index': {}}, {'control_input': {}}, {'control_index': {}}, {'vcf': {}}, {'tbi': {}}], [{'meta2': {}}, {'bed': {}}, {'pon_path': {}}]] -[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("severus.log") , emit: log - tuple val(meta), path("read_qual.txt") , emit: read_qual - tuple val(meta), path("breakpoints_double.csv") , emit: breakpoints_double - tuple val(meta), path("read_alignments") , emit: read_alignments , optional: true - tuple val(meta), path("read_ids.csv") , emit: read_ids , optional: true - tuple val(meta), path("severus_collaped_dup.bed") , emit: collapsed_dup , optional: true - tuple val(meta), path("severus_LOH.bed") , emit: loh , optional: true - tuple val(meta), path("all_SVs/severus_all.vcf.gz") , emit: all_vcf , optional: true - tuple val(meta), path("all_SVs/severus_all.vcf.gz.tbi") , emit: all_tbi , optional: true - tuple val(meta), path("all_SVs/breakpoint_clusters_list.tsv") , emit: all_breakpoints_clusters_list , optional: true - tuple val(meta), path("all_SVs/breakpoint_clusters.tsv") , emit: all_breakpoints_clusters , optional: true - tuple val(meta), path("all_SVs/plots/severus_*.html") , emit: all_plots , optional: true - tuple val(meta), path("somatic_SVs/severus_somatic.vcf.gz") , emit: somatic_vcf //, optional: true - tuple val(meta), path("somatic_SVs/severus_somatic.vcf.gz.tbi") , emit: somatic_tbi , optional: true - tuple val(meta), path("somatic_SVs/breakpoint_clusters_list.tsv") , emit: somatic_breakpoints_clusters_list, optional: true - tuple val(meta), path("somatic_SVs/breakpoint_clusters.tsv") , emit: somatic_breakpoints_clusters , optional: true - tuple val(meta), path("somatic_SVs/plots/severus_*.html") , emit: somatic_plots , optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Found 18 outputs in modules/nf-core/severus/main.nf -[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Outputs: {'log': [[{'meta': {}}, {'severus.log': {}}]], 'read_qual': [[{'meta': {}}, {'read_qual.txt': {}}]], 'breakpoints_double': [[{'meta': {}}, {'breakpoints_double.csv': {}}]], 'read_alignments': [[{'meta': {}}, {'read_alignments': {}}]], 'read_ids': [[{'meta': {}}, {'read_ids.csv': {}}]], 'collapsed_dup': [[{'meta': {}}, {'severus_collaped_dup.bed': {}}]], 'loh': [[{'meta': {}}, {'severus_LOH.bed': {}}]], 'all_vcf': [[{'meta': {}}, {'all_SVs/severus_all.vcf.gz': {}}]], 'all_tbi': [[{'meta': {}}, {'all_SVs/severus_all.vcf.gz.tbi': {}}]], 'all_breakpoints_clusters_list': [[{'meta': {}}, {'all_SVs/breakpoint_clusters_list.tsv': {}}]], 'all_breakpoints_clusters': [[{'meta': {}}, {'all_SVs/breakpoint_clusters.tsv': {}}]], 'all_plots': [[{'meta': {}}, {'all_SVs/plots/severus_*.html': {}}]], 'somatic_vcf': [[{'meta': {}}, {'somatic_SVs/severus_somatic.vcf.gz': {}}]], 'somatic_tbi': [[{'meta': {}}, {'somatic_SVs/severus_somatic.vcf.gz.tbi': {}}]], 'somatic_breakpoints_clusters_list': [[{'meta': {}}, {'somatic_SVs/breakpoint_clusters_list.tsv': {}}]], 'somatic_breakpoints_clusters': [[{'meta': {}}, {'somatic_SVs/breakpoint_clusters.tsv': {}}]], 'somatic_plots': [[{'meta': {}}, {'somatic_SVs/plots/severus_*.html': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("severus.log") , emit: log - tuple val(meta), path("read_qual.txt") , emit: read_qual - tuple val(meta), path("breakpoints_double.csv") , emit: breakpoints_double - tuple val(meta), path("read_alignments") , emit: read_alignments , optional: true - tuple val(meta), path("read_ids.csv") , emit: read_ids , optional: true - tuple val(meta), path("severus_collaped_dup.bed") , emit: collapsed_dup , optional: true - tuple val(meta), path("severus_LOH.bed") , emit: loh , optional: true - tuple val(meta), path("all_SVs/severus_all.vcf.gz") , emit: all_vcf , optional: true - tuple val(meta), path("all_SVs/severus_all.vcf.gz.tbi") , emit: all_tbi , optional: true - tuple val(meta), path("all_SVs/breakpoint_clusters_list.tsv") , emit: all_breakpoints_clusters_list , optional: true - tuple val(meta), path("all_SVs/breakpoint_clusters.tsv") , emit: all_breakpoints_clusters , optional: true - tuple val(meta), path("all_SVs/plots/severus_*.html") , emit: all_plots , optional: true - tuple val(meta), path("somatic_SVs/severus_somatic.vcf.gz") , emit: somatic_vcf //, optional: true - tuple val(meta), path("somatic_SVs/severus_somatic.vcf.gz.tbi") , emit: somatic_tbi , optional: true - tuple val(meta), path("somatic_SVs/breakpoint_clusters_list.tsv") , emit: somatic_breakpoints_clusters_list, optional: true - tuple val(meta), path("somatic_SVs/breakpoint_clusters.tsv") , emit: somatic_breakpoints_clusters , optional: true - tuple val(meta), path("somatic_SVs/plots/severus_*.html") , emit: somatic_plots , optional: true - path "versions.yml" , emit: versions - - -[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/severus/main.nf -[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:52:38,674] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:38,674] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:38,880] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:38,892] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:38,892] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:38,893] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:38,893] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:39,092] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:39,096] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/severus'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:39,097] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/severus'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:39,214] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:39,367] nf_core.components.components_differ [DEBUG ] Applying patch to modules/nf-core/severus/main.nf -[2025-11-27 15:52:39,367] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:39,368] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:39,435] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:39,448] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:39,448] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:39,449] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:39,449] git.cmd [DEBUG ] Popen(['git', 'checkout', '81880787133db07d9b4c1febd152c090eb8325dc'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:49,232] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/untar/main.nf -[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'archive': {}}]] -[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("${prefix}"), emit: untar - path "versions.yml", emit: versions - - -[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/untar/main.nf -[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Outputs: {'untar': [[{'meta': {}}, {'${prefix}': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("${prefix}"), emit: untar - path "versions.yml", emit: versions - - -[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/untar/main.nf -[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:52:57,845] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:57,845] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:58,185] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:58,197] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:58,198] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:58,198] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:58,199] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:58,243] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:58,246] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/untar'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:58,247] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/untar'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:58,344] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:52:58,548] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:52:58,549] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:58,620] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:52:58,633] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:52:58,633] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:52:58,634] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:52:58,634] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:01,667] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:05,409] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/unzip/main.nf -[2025-11-27 15:53:05,409] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'archive': {}}]] -[2025-11-27 15:53:05,409] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("${prefix}/"), emit: unzipped_archive - path "versions.yml" , emit: versions - - -[2025-11-27 15:53:05,409] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/unzip/main.nf -[2025-11-27 15:53:05,409] nf_core.components.nfcore_component [DEBUG ] Outputs: {'unzipped_archive': [[{'meta': {}}, {'${prefix}/': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:53:05,410] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("${prefix}/"), emit: unzipped_archive - path "versions.yml" , emit: versions - - -[2025-11-27 15:53:05,410] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/unzip/main.nf -[2025-11-27 15:53:05,410] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:53:05,410] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:53:05,411] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:05,637] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:05,649] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:53:05,649] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:53:05,649] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:53:05,650] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:05,794] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:53:05,798] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/unzip'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:05,799] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/unzip'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:05,893] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:53:06,081] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:53:06,082] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:06,193] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:06,205] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:53:06,205] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:53:06,206] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:53:06,206] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:09,447] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:13,327] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/wget/main.nf -[2025-11-27 15:53:13,327] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'url': {}}]] -[2025-11-27 15:53:13,327] nf_core.components.nfcore_component [DEBUG ] Found output_data: - tuple val(meta), path("${prefix}.${suffix}"), emit: outfile - path "versions.yml" , emit: versions - - -[2025-11-27 15:53:13,327] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/wget/main.nf -[2025-11-27 15:53:13,327] nf_core.components.nfcore_component [DEBUG ] Outputs: {'outfile': [[{'meta': {}}, {'${prefix}.${suffix}': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:53:13,328] nf_core.components.nfcore_component [DEBUG ] Output data: - tuple val(meta), path("${prefix}.${suffix}"), emit: outfile - path "versions.yml" , emit: versions - - -[2025-11-27 15:53:13,328] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/wget/main.nf -[2025-11-27 15:53:13,328] nf_core.components.nfcore_component [DEBUG ] Topics: {} -[2025-11-27 15:53:13,328] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:53:13,328] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:13,447] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:13,458] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:53:13,459] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:53:13,459] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:53:13,460] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:13,563] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:53:13,567] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/wget'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:13,568] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/wget'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:13,684] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:53:13,841] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:53:13,842] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:13,932] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:13,943] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:53:13,944] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:53:13,944] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:53:13,944] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:16,975] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:21,106] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:53:21,107] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:21,393] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:21,417] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:53:21,418] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:53:21,418] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:53:21,420] git.cmd [DEBUG ] Popen(['git', 'checkout', '05954dab2ff481bcb999f24455da29a5828af08d'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:27,600] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:38,141] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:53:38,142] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:38,286] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:38,298] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:53:38,298] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:53:38,298] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:53:38,299] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:38,354] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:53:38,358] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'subworkflows/nf-core/bam_stats_samtools'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:38,372] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:53:38,458] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:53:38,459] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:38,517] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:38,528] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:53:38,529] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:53:38,529] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:53:38,530] git.cmd [DEBUG ] Popen(['git', 'checkout', 'c2b22d85f30a706a3073387f30380704fcae013b'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:53:51,273] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:04,283] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:54:04,285] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:05,104] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:05,146] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:54:05,149] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:54:05,150] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:54:05,154] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:05,466] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:54:05,484] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'subworkflows/nf-core/utils_nextflow_pipeline'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:05,611] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:54:05,766] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:54:05,768] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:05,968] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:06,009] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:54:06,011] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:54:06,012] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:54:06,013] git.cmd [DEBUG ] Popen(['git', 'checkout', '51ae5406a030d4da1e49e4dab49756844fdd6c7a'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:43,965] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:57,578] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:54:57,578] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:57,881] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:57,895] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:54:57,895] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:54:57,896] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:54:57,897] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:58,070] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:54:58,074] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'subworkflows/nf-core/utils_nfcore_pipeline'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:58,084] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:54:58,172] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:54:58,173] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:58,226] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:54:58,240] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:54:58,241] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:54:58,241] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:54:58,241] git.cmd [DEBUG ] Popen(['git', 'checkout', '2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:55:06,742] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:55:16,344] git.util [DEBUG ] sys.platform='linux', git_executable='git' -[2025-11-27 15:55:16,344] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:55:16,558] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:55:16,572] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path -[2025-11-27 15:55:16,573] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json -[2025-11-27 15:55:16,573] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml -[2025-11-27 15:55:16,574] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:55:16,711] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:55:16,716] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'subworkflows/nf-core/utils_nfschema_plugin'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) -[2025-11-27 15:55:16,727] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) -[2025-11-27 15:55:16,820] nf_core.pipelines.lint [DEBUG ] Printing final results -[2025-11-27 15:55:16,821] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,821] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,821] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,821] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,821] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,821] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,821] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,821] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,821] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,822] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,822] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,822] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,822] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,822] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,822] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,822] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,822] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,822] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,823] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,823] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,823] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,823] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,823] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,823] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,823] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,823] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,823] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,823] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,823] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,823] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,824] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,824] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,824] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,824] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,824] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,824] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,824] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,824] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,824] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,824] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,825] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,826] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,827] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,827] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,827] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,827] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,827] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,827] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,827] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,827] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,827] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,827] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,828] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,829] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,830] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,831] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,832] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,833] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,834] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,834] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,834] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,834] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,834] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,834] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,834] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,834] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,834] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,834] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,835] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,836] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,836] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,836] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,839] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,839] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,839] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,839] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,839] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,839] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,839] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,839] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,839] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,839] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,840] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,841] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,841] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,841] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,841] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,841] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,841] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,841] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,841] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,841] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,841] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,841] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,842] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,843] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,843] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,843] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,843] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,843] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,843] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,843] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,843] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,843] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,843] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,843] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,844] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,845] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,845] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,845] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,845] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,845] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,845] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,845] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,845] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,845] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,845] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,845] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,845] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,846] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,847] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,848] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,848] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,848] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,848] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,848] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,848] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,848] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,848] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,848] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,848] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,848] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,848] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,849] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,850] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,851] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,852] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,853] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,853] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,853] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,853] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,853] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,853] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,853] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,853] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,853] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,853] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,853] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,854] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,855] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,856] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,857] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,858] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,858] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,858] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,858] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,858] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,858] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,858] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,858] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,858] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,858] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,858] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,858] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,859] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,860] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,861] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,862] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,863] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,864] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,865] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,866] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,867] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,868] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,868] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,868] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,868] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,868] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,868] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,868] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,868] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,868] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,868] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,869] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,870] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,870] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,870] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,870] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,870] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,870] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,870] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,870] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,870] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,870] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,870] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,870] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,871] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,872] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,873] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,873] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,873] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,873] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,873] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,873] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,873] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,873] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,873] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,873] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,873] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,874] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,875] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,876] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,877] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,878] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,878] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,878] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,878] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,878] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,878] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,878] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,878] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,878] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,878] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,878] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,878] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,879] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,880] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,880] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,880] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,880] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,880] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,880] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,880] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,880] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,880] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,880] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,880] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,880] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,881] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,882] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,883] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,883] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,883] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,883] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,883] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,883] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,883] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,883] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,883] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,883] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,883] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,884] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,885] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,885] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,885] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,885] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,885] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,885] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,885] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,885] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,885] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,885] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,886] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,887] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,888] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,889] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,890] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,891] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,892] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,892] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,892] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,892] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,892] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,892] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,892] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,892] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,892] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,892] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,893] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,894] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,895] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,896] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,897] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,897] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,897] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,897] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,897] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,897] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,897] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,897] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,897] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,897] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,898] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,899] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,900] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,901] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,902] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,902] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,902] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,902] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,902] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,902] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,902] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,902] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,902] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,902] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,902] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,903] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,904] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,905] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,906] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,907] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,907] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,907] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,907] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,907] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,907] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,907] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,907] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,907] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,907] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,907] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,907] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,908] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,909] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,910] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,911] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,912] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,913] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,914] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,915] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,915] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,915] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,915] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,915] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,915] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,915] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,915] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,915] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,915] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,916] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,917] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,918] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,919] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,920] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,921] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,922] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,923] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,923] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,923] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,923] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,923] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,923] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,923] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,923] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,923] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,923] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,923] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,924] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,925] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,926] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,927] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,947] nf_core.components.lint [DEBUG ] Printing final results -[2025-11-27 15:55:16,948] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,948] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,948] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,948] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,948] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,948] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,948] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,948] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,948] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,948] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,949] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,950] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,950] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,950] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,950] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,950] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,950] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,950] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,950] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,950] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,950] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,951] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,952] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,953] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,954] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,955] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,955] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,955] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,955] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,955] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,955] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,955] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,955] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,955] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,955] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,956] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,957] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,957] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,957] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,957] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,957] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,957] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,957] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,957] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,957] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,957] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,958] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,959] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,960] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,960] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,960] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,960] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,968] nf_core.components.lint [DEBUG ] Printing final results -[2025-11-27 15:55:16,969] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,969] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,969] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,969] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,969] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,969] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,969] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,969] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,969] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,969] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,970] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,971] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,972] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,973] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,973] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,973] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,973] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,973] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,973] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,973] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,973] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,973] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,973] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,973] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,973] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,974] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,975] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,975] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,975] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,975] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,975] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,975] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,975] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,975] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,975] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,975] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,975] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,976] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,977] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,978] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,979] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,979] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,979] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,979] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,979] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,979] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,979] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,979] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,979] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,979] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,980] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,981] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,981] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,981] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,981] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,981] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,981] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,981] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,981] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,981] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,981] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,982] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,983] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,983] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,983] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,983] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,983] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,983] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,983] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,983] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,983] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,983] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,984] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,985] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,985] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,985] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,985] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,985] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,985] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,985] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,985] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,985] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,985] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,986] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,987] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,987] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,987] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,987] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,987] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,987] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,987] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,987] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,987] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,987] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,988] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,989] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,989] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,989] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,989] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,989] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,989] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,989] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,989] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,989] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,989] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,990] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,990] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,990] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,990] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,990] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,990] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,990] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,990] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,990] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,990] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,990] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,990] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,990] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,990] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,990] markdown_it.rules_block.list [DEBUG 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[DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False -[2025-11-27 15:55:16,993] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False diff --git a/modules/local/cramino/meta.yml b/modules/local/cramino/meta.yml index 93fbea6c..2c2fd2d7 100644 --- a/modules/local/cramino/meta.yml +++ b/modules/local/cramino/meta.yml @@ -1,7 +1,6 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "cramino" -## TODO nf-core: Add a description of the module and list keywords description: A tool for quick quality assessment of cram and bam files, intended for long read sequencing. keywords: - quality diff --git a/modules/local/sigprofiler/matrixgenerator/tests/main.nf.test b/modules/local/sigprofiler/matrixgenerator/tests/main.nf.test index 564d3230..87daee4b 100644 --- a/modules/local/sigprofiler/matrixgenerator/tests/main.nf.test +++ b/modules/local/sigprofiler/matrixgenerator/tests/main.nf.test @@ -20,7 +20,7 @@ nextflow_process { setup { run("PREPARE_SIGNATURES") { - script "../../../../../subworkflows/local/prepare_signatures.nf" + script "../../../../../subworkflows/local/prepare_signatures/main.nf" workflow { """ input[0] = 'CHM13-T2T' diff --git a/nextflow.config b/nextflow.config index 24edbd9b..adc6b318 100644 --- a/nextflow.config +++ b/nextflow.config @@ -9,7 +9,6 @@ // Global default params, used in configs params { - // TODO nf-core: Specify your pipeline's command line flags // Input options input = null @@ -401,7 +400,6 @@ dag { manifest { name = 'IntGenomicsLab/lrsomatic' contributors = [ - // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0 [ name: 'Luuk Harbers', affiliation: 'VIB Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory of Integrative Cancer Genomics, Department of Oncology, KU Leuven, Leuven, Belgium; VIB Center for AI and Computational Biology, VIB, Leuven, Belgium', @@ -472,7 +470,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'main' nextflowVersion = '!>=25.10.4' - version = '1.1.0' + version = '1.2.0dev' doi = '' diagram = 'assets/lrsomatic_1.0.png' } diff --git a/nextflow_schema.json b/nextflow_schema.json index 04f31ded..893a4690 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -111,7 +111,8 @@ "fa_icon": "fas fa-filter" }, "generate_gvcf": { - "type": "boolean" + "type": "boolean", + "description": "Also write gVCFs from DeepVariant and DeepSomatic, and publish them next to the VCFs." } } }, @@ -224,7 +225,8 @@ "default": "", "properties": { "autocorrelation": { - "type": "string" + "type": "string", + "description": "Pass --acf to fibertools qc to add the nucleosome autocorrelation to the Fiber-seq QC output. Any non-empty value turns it on." } } }, @@ -259,10 +261,12 @@ "description": "Download the VEP cache if not already present" }, "vep_custom": { - "type": "string" + "type": "string", + "description": "Path to a bgzipped VCF (.vcf.gz) of custom variants for VEP to annotate against. Needs a matching --custom file=... entry in --vep_args." }, "vep_custom_tbi": { - "type": "string" + "type": "string", + "description": "Path to the tabix index of --vep_custom." }, "vep_alphamissense": { "type": "string", @@ -384,7 +388,8 @@ "properties": { "severus_minsupport": { "type": "integer", - "default": 3 + "default": 3, + "description": "Minimum number of supporting reads for Severus to report an SV (Severus --min-support)." }, "severus_whitelist": { "type": "string", @@ -584,7 +589,8 @@ "default": "", "properties": { "wakhan_chroms": { - "type": "string" + "type": "string", + "description": "Comma-separated contigs, or ranges such as chr1-22,chrX, for Wakhan to use. Defaults to chr1-22,chrX for female samples and chr1-22,chrX,chrY for male samples." } } }, @@ -675,6 +681,10 @@ "type": "boolean", "description": "Skips wakhan" }, + "skip_modkit": { + "type": "boolean", + "description": "Skip the modkit pileup of base modifications." + }, "skip_fiber": { "type": "boolean", "description": "Skip Fibertools steps" @@ -1039,10 +1049,5 @@ { "$ref": "#/$defs/generic_options" } - ], - "properties": { - "skip_modkit": { - "type": "boolean" - } - } + ] } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 47ba8849..55848112 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -15,9 +15,9 @@ "@id": "https://w3id.org/ro/wftest/0.2" } ], - "creativeWorkStatus": "Stable", - "datePublished": "2026-10-28T09:47:28+00:00", - "description": "# IntGenomicsLab/lrsomatic\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/IntGenomicsLab/lrsomatic)\n[![GitHub Actions CI Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.17751829-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.17751829)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.2.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.2.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/IntGenomicsLab/lrsomatic)\n\n## Introduction\n\n**IntGenomicsLab/lrsomatic** is a robust bioinformatics pipeline designed for processing and analyzing **somatic DNA sequencing** data for long-read sequencing technologies from **Oxford Nanopore** and **PacBio**. It supports both canonical base DNA and modified base calling, including specialized applications such as **Fiber-seq**.\n\nThis **end-to-end pipeline** handles the entire workflow — **from raw read processing and alignment, to comprehensive somatic variant calling**, including single nucleotide variants, indels, structural variants, copy number alterations, and modified bases.\n\nIt can be run in both **matched tumour-normal** and **tumour-only mode**, offering flexibility depending on the users study design.\n\nDeveloped using **Nextflow DSL2**, it offers high portability and scalability across diverse computing environments. By leveraging Docker or Singularity containers, installation is streamlined and results are highly reproducible. Each process runs in an isolated container, simplifying dependency management and updates. Where applicable, pipeline components are sourced from **nf-core/modules**, promoting reuse, interoperability, and consistency within the broader Nextflow and nf-core ecosystems.\n\nFor more information on how to run the pipeline, you can also go [here](https://intgenomicslab.github.io/lrsomatic).\n\n## Pipeline summary\n\n![image](./assets/lrsomatic_1.0.png)\n\n**1) Pre-processing:**\n\na. Raw read QC ([`cramino`](https://github.com/wdecoster/cramino))\n\nb. Alignment to the reference genome ([`minimap2`](https://github.com/lh3/minimap2))\n\nc. Post alignment QC ([`cramino`](https://github.com/wdecoster/cramino), [`samtools idxstats`](https://github.com/samtools/samtools), [`samtools flagstats`](https://github.com/samtools/samtools), [`samtools stats`](https://github.com/samtools/samtools))\n\nd. Specific for calling modified base calling ([`Modkit`](https://github.com/nanoporetech/modkit), [`Fibertools`](https://github.com/fiberseq/fibertools-rs))\n\n**2i) Matched mode: small variant calling:**\n\na. Calling Germline SNPs ([`Clair3`](https://github.com/HKU-BAL/Clair3))\n\nb. Phasing and Haplotagging the SNPs in the normal and tumour BAM ([`LongPhase`](https://github.com/twolinin/longphase))\n\nc. Calling somatic SNVs ([`ClairS`](https://github.com/HKU-BAL/ClairS))\n\n**2ii) Tumour only mode: small variant calling:**\n\na. Calling Germline SNPs and somatic SNVs ([`ClairS-TO`](https://github.com/HKU-BAL/ClairS-TO))\n\nb. Phasing and Haplotagging germline SNPs in tumour BAM ([`LongPhase`](https://github.com/twolinin/longphase))\n\n**3) Large variant calling:**\n\na. Somatic structural variant calling ([`Severus`](https://github.com/KolmogorovLab/Severus))\n\nb. Somatic structural variant and copy-number calling ([`SAVANA`](https://github.com/cortes-ciriano-lab/savana))\n\nc. Copy number alterion calling; long read version of ([`ASCAT`](https://github.com/VanLoo-lab/ascat))\n\n**4) Annotation:**\n\na. Small variant annotation ([`VEP`](https://github.com/Ensembl/ensembl-vep)), with pathogenicity and clinical-significance plugins: [`AlphaMissense`](https://github.com/google-deepmind/alphamissense), [`ClinVar`](https://www.ncbi.nlm.nih.gov/clinvar/), [`REVEL`](https://sites.google.com/site/revelgenomics/), [`SIFT`/`PolyPhen`](https://github.com/Ensembl/VEP_plugins), and optionally [`CADD`](https://cadd.gs.washington.edu/) and [`EVE`](https://evemodel.org/)\n\nb. Structural variant annotation ([`VEP`](https://github.com/Ensembl/ensembl-vep))\n\nc. Somatic SV and CNA functional annotation ([`Padfoot`](https://github.com/KolmogorovLab/Padfoot))\n\n**5) Visualisation:**\n\na. Rearrangement and copy-number figures per CN/SV caller pair ([`ReConPlot`](https://github.com/cortes-ciriano-lab/ReConPlot))\n\n\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst prepare a samplesheet with your input data that looks as follows:\n\n```csv\nsample,bam_tumor,bam_normal,platform,sex,fiber\nsample1,tumour.bam,normal.bam,ont,female,n\nsample2,tumour.bam,,ont,female,y\nsample3,tumour.bam,,pb,male,n\nsample4,tumour.bam,normal.bam,pb,male,y\n```\n\nEach row is a sample. BAMs must be unaligned, all fields except `bam_normal` are required, and an empty `bam_normal` runs the sample in tumour-only mode. `platform` is `ont` or `pb`, `sex` is `female` or `male`, and `fiber` is `y` or `n` for Fiber-seq; see the [usage documentation](/docs/usage.md#full-description-of-samplesheet-columns).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run IntGenomicsLab/lrsomatic \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\nMore detail is given in our [usage documentation](/docs/usage.md)\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\n## Credits\n\nIntGenomicsLab/lr_somatic was originally written by Luuk Harbers, Robert Forsyth, Amber Verhasselt, Alexandra Pančíková, Marios Eftychiou, Ruben Cools, Laurens Lambrechts, and Jonas Demeulemeester.\n\n## Pipeline output\n\nThe main output is an aligned and phased tumour BAM, per-sample QC from `cramino`, `mosdepth`, `samtools` and optionally `fibertools`, a MultiQC report, and a self-contained per-sample HTML report (`/report/_report.html`; disable it with `--skip_report`).\n\nVariant and copy number callers (`clairS`, `clairS-TO`, `severus`, `savana`, `ascat`) write to their own folders; Padfoot annotations and ReConPlot figures go to `padfoot/` and `reconplot/`, one subfolder per caller pair. See the [output documentation](/docs/output.md).\n\nExample output directory structure:\n\n```\n├── Sample 1\n│ ├── ascat\n│ ├── bamfiles\n│ ├── padfoot\n│ │ ├── savana\n│ │ └── severus_wakhan\n│ ├── qc\n│ │ ├── tumor\n│ │ │ ├── cramino_aln\n│ │ │ ├── cramino_ubam\n│ │ │ ├── fibertoolsrs\n│ │ │ ├── mosdepth\n│ │ │ ├── samtools\n│ ├── reconplot\n│ │ ├── savana\n│ │ ├── severus_ascat\n│ │ └── severus_wakhan\n│ ├── variants\n│ │ ├──clairS-TO\n│ │ ├──severus\n│ │ ├──savana\n│ ├── vep\n│ │ ├── germline\n│ │ ├── somatic\n│ │ ├── SVs\n│ ├── report\n│\n├── Sample 2\n│ ├── ascat\n│ ├── bamfiles\n│ ├── padfoot\n│ │ ├── savana\n│ │ └── severus_wakhan\n│ ├── qc\n│ │ ├── tumor\n│ │ │ ├── cramino_aln\n│ │ │ ├── cramino_ubam\n│ │ │ ├── fibertoolsrs\n│ │ │ ├── mosdepth\n│ │ │ ├── samtools\n│ │ ├── normal\n│ │ │ ├── cramino_aln\n│ │ │ ├── cramino_ubam\n│ │ │ ├── fibertoolsrs\n│ │ │ ├── mosdepth\n│ │ │ ├── samtools\n│ ├── reconplot\n│ │ ├── savana\n│ │ ├── severus_ascat\n│ │ └── severus_wakhan\n│ ├── variants\n│ │ ├── clair3\n│ │ ├── clairS\n│ │ ├── severus\n│ │ ├── savana\n│ ├── vep\n│ │ ├── germline\n│ │ ├── somatic\n│ │ ├── SVs\n├── pipeline_info\n```\n\nmore detail is given in our [output documentation](/docs/output.md)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\n## Citations\n\nIf you use `IntGenomicsLab/lrsomatic` for your analysis, please cite it using the following:\n\n> LRSomatic: a highly scalable and robust pipeline for somatic variant calling in long-read sequencing data\n>\n> Robert A. Forsyth*, Luuk Harbers*, Amber Verhasselt, Ana-Lucía Rocha Iraizós, Sidi Yang, Joris Vande Velde, Christopher Davies, Nischalan Pillay, Laurens Lambrechts, Jonas Demeulemeester\n>\n> bioRxiv 2026.02.26.707772; doi: https://doi.org/10.64898/2026.02.26.707772\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "creativeWorkStatus": "InProgress", + "datePublished": "2026-10-29T12:23:13+00:00", + "description": "# IntGenomicsLab/lrsomatic\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/IntGenomicsLab/lrsomatic)\n[![GitHub Actions CI Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.17751829-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.17751829)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.2.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.2.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/IntGenomicsLab/lrsomatic)\n\n## Introduction\n\n**IntGenomicsLab/lrsomatic** is a robust bioinformatics pipeline designed for processing and analyzing **somatic DNA sequencing** data for long-read sequencing technologies from **Oxford Nanopore** and **PacBio**. It supports both canonical base DNA and modified base calling, including specialized applications such as **Fiber-seq**.\n\nThis **end-to-end pipeline** handles the entire workflow — **from raw read processing and alignment, to comprehensive somatic variant calling**, including single nucleotide variants, indels, structural variants, copy number alterations, and modified bases.\n\nIt can be run in both **matched tumour-normal** and **tumour-only mode**, offering flexibility depending on the users study design.\n\nDeveloped using **Nextflow DSL2**, it offers high portability and scalability across diverse computing environments. By leveraging Docker or Singularity containers, installation is streamlined and results are highly reproducible. Each process runs in an isolated container, simplifying dependency management and updates. Where applicable, pipeline components are sourced from **nf-core/modules**, promoting reuse, interoperability, and consistency within the broader Nextflow and nf-core ecosystems.\n\nFor more information on how to run the pipeline, you can also go [here](https://intgenomicslab.github.io/lrsomatic).\n\n## Pipeline summary\n\n![image](./assets/lrsomatic_1.0.png)\n\n**1) Pre-processing:**\n\na. Raw read QC ([`cramino`](https://github.com/wdecoster/cramino))\n\nb. Alignment to the reference genome ([`minimap2`](https://github.com/lh3/minimap2))\n\nc. Post alignment QC ([`cramino`](https://github.com/wdecoster/cramino), [`samtools idxstats`](https://github.com/samtools/samtools), [`samtools flagstats`](https://github.com/samtools/samtools), [`samtools stats`](https://github.com/samtools/samtools))\n\nd. Specific for calling modified base calling ([`Modkit`](https://github.com/nanoporetech/modkit), [`Fibertools`](https://github.com/fiberseq/fibertools-rs))\n\n**2i) Matched mode: small variant calling:**\n\na. Calling Germline SNPs ([`Clair3`](https://github.com/HKU-BAL/Clair3))\n\nb. Phasing and Haplotagging the SNPs in the normal and tumour BAM ([`LongPhase`](https://github.com/twolinin/longphase))\n\nc. Calling somatic SNVs ([`ClairS`](https://github.com/HKU-BAL/ClairS))\n\n**2ii) Tumour only mode: small variant calling:**\n\na. Calling Germline SNPs and somatic SNVs ([`ClairS-TO`](https://github.com/HKU-BAL/ClairS-TO))\n\nb. Phasing and Haplotagging germline SNPs in tumour BAM ([`LongPhase`](https://github.com/twolinin/longphase))\n\n**3) Large variant calling:**\n\na. Somatic structural variant calling ([`Severus`](https://github.com/KolmogorovLab/Severus))\n\nb. Somatic structural variant and copy-number calling ([`SAVANA`](https://github.com/cortes-ciriano-lab/savana))\n\nc. Copy number alterion calling; long read version of ([`ASCAT`](https://github.com/VanLoo-lab/ascat))\n\n**4) Annotation:**\n\na. Small variant annotation ([`VEP`](https://github.com/Ensembl/ensembl-vep)), with pathogenicity and clinical-significance plugins: [`AlphaMissense`](https://github.com/google-deepmind/alphamissense), [`ClinVar`](https://www.ncbi.nlm.nih.gov/clinvar/), [`REVEL`](https://sites.google.com/site/revelgenomics/), [`SIFT`/`PolyPhen`](https://github.com/Ensembl/VEP_plugins), and optionally [`CADD`](https://cadd.gs.washington.edu/) and [`EVE`](https://evemodel.org/)\n\nb. Structural variant annotation ([`VEP`](https://github.com/Ensembl/ensembl-vep))\n\nc. Somatic SV and CNA functional annotation ([`Padfoot`](https://github.com/KolmogorovLab/Padfoot))\n\n**5) Visualisation:**\n\na. Rearrangement and copy-number figures per CN/SV caller pair ([`ReConPlot`](https://github.com/cortes-ciriano-lab/ReConPlot))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst prepare a samplesheet with your input data that looks as follows:\n\n```csv\nsample,bam_tumor,bam_normal,platform,sex,fiber\nsample1,tumour.bam,normal.bam,ont,female,n\nsample2,tumour.bam,,ont,female,y\nsample3,tumour.bam,,pb,male,n\nsample4,tumour.bam,normal.bam,pb,male,y\n```\n\nEach row is a sample. BAMs must be unaligned, all fields except `bam_normal` are required, and an empty `bam_normal` runs the sample in tumour-only mode. `platform` is `ont` or `pb`, `sex` is `female` or `male`, and `fiber` is `y` or `n` for Fiber-seq; see the [usage documentation](/docs/usage.md#full-description-of-samplesheet-columns).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run IntGenomicsLab/lrsomatic \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\nMore detail is given in our [usage documentation](/docs/usage.md)\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\n## Credits\n\nIntGenomicsLab/lr_somatic was originally written by Luuk Harbers, Robert Forsyth, Amber Verhasselt, Alexandra Pančíková, Marios Eftychiou, Ruben Cools, Laurens Lambrechts, and Jonas Demeulemeester.\n\n## Pipeline output\n\nThe main output is an aligned and phased tumour BAM, per-sample QC from `cramino`, `mosdepth`, `samtools` and optionally `fibertools`, a MultiQC report, and a self-contained per-sample HTML report (`/report/_report.html`; disable it with `--skip_report`).\n\nVariant and copy number callers (`clairS`, `clairS-TO`, `severus`, `savana`, `ascat`) write to their own folders; Padfoot annotations and ReConPlot figures go to `padfoot/` and `reconplot/`, one subfolder per caller pair. See the [output documentation](/docs/output.md).\n\nExample output directory structure:\n\n```\n├── Sample 1\n│ ├── ascat\n│ ├── bamfiles\n│ ├── padfoot\n│ │ ├── savana\n│ │ └── severus_wakhan\n│ ├── qc\n│ │ ├── tumor\n│ │ │ ├── cramino_aln\n│ │ │ ├── cramino_ubam\n│ │ │ ├── fibertoolsrs\n│ │ │ ├── mosdepth\n│ │ │ ├── samtools\n│ ├── reconplot\n│ │ ├── savana\n│ │ ├── severus_ascat\n│ │ └── severus_wakhan\n│ ├── variants\n│ │ ├──clairS-TO\n│ │ ├──severus\n│ │ ├──savana\n│ ├── vep\n│ │ ├── germline\n│ │ ├── somatic\n│ │ ├── SVs\n│ ├── report\n│\n├── Sample 2\n│ ├── ascat\n│ ├── bamfiles\n│ ├── padfoot\n│ │ ├── savana\n│ │ └── severus_wakhan\n│ ├── qc\n│ │ ├── tumor\n│ │ │ ├── cramino_aln\n│ │ │ ├── cramino_ubam\n│ │ │ ├── fibertoolsrs\n│ │ │ ├── mosdepth\n│ │ │ ├── samtools\n│ │ ├── normal\n│ │ │ ├── cramino_aln\n│ │ │ ├── cramino_ubam\n│ │ │ ├── fibertoolsrs\n│ │ │ ├── mosdepth\n│ │ │ ├── samtools\n│ ├── reconplot\n│ │ ├── savana\n│ │ ├── severus_ascat\n│ │ └── severus_wakhan\n│ ├── variants\n│ │ ├── clair3\n│ │ ├── clairS\n│ │ ├── severus\n│ │ ├── savana\n│ ├── vep\n│ │ ├── germline\n│ │ ├── somatic\n│ │ ├── SVs\n├── pipeline_info\n```\n\nmore detail is given in our [output documentation](/docs/output.md)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\n## Citations\n\nIf you use `IntGenomicsLab/lrsomatic` for your analysis, please cite it using the following:\n\n> LRSomatic: a highly scalable and robust pipeline for somatic variant calling in long-read sequencing data\n>\n> Robert A. Forsyth*, Luuk Harbers*, Amber Verhasselt, Ana-Lucía Rocha Iraizós, Sidi Yang, Joris Vande Velde, Christopher Davies, Nischalan Pillay, Laurens Lambrechts, Jonas Demeulemeester\n>\n> bioRxiv 2026.02.26.707772; doi: https://doi.org/10.64898/2026.02.26.707772\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -93,7 +93,7 @@ }, "mentions": [ { - "@id": "#97291dab-36c6-4b95-b3ba-9d715c953af5" + "@id": "#a31a4ee9-5087-4832-8fbd-821dbf0fc102" } ], "name": "IntGenomicsLab/lrsomatic" @@ -144,7 +144,7 @@ } ], "dateCreated": "", - "dateModified": "2026-10-28T10:47:28Z", + "dateModified": "2026-10-29T13:23:13Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -172,10 +172,10 @@ }, "url": [ "https://github.com/IntGenomicsLab/lrsomatic", - "https://nf-co.re/IntGenomicsLab/lrsomatic/1.1.0/" + "https://nf-co.re/IntGenomicsLab/lrsomatic/dev/" ], "version": [ - "1.1.0" + "1.2.0dev" ] }, { @@ -200,11 +200,11 @@ "version": "1.1" }, { - "@id": "#97291dab-36c6-4b95-b3ba-9d715c953af5", + "@id": "#a31a4ee9-5087-4832-8fbd-821dbf0fc102", "@type": "TestSuite", "instance": [ { - "@id": "#65d87ca4-0d27-4af3-8b1a-875becab8174" + "@id": "#1e5ff16e-ac97-4932-ac17-6abc6d495529" } ], "mainEntity": { @@ -222,7 +222,7 @@ "version": "0.2" }, { - "@id": "#65d87ca4-0d27-4af3-8b1a-875becab8174", + "@id": "#1e5ff16e-ac97-4932-ac17-6abc6d495529", "@type": "TestInstance", "name": "GitHub Actions workflow for testing IntGenomicsLab/lrsomatic", "resource": "repos/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml", diff --git a/subworkflows/local/deepsomatic.nf b/subworkflows/local/deepsomatic/main.nf similarity index 90% rename from subworkflows/local/deepsomatic.nf rename to subworkflows/local/deepsomatic/main.nf index 1bb5d86c..58acf3d4 100644 --- a/subworkflows/local/deepsomatic.nf +++ b/subworkflows/local/deepsomatic/main.nf @@ -1,6 +1,6 @@ -include { DEEPSOMATIC_MAKEEXAMPLES } from '../../modules/local/deepsomatic/makeexamples/main' -include { DEEPSOMATIC_CALLVARIANTS } from '../../modules/local/deepsomatic/callvariants/main' -include { DEEPSOMATIC_POSTPROCESSVARIANTS } from '../../modules/local/deepsomatic/postprocessvariants/main' +include { DEEPSOMATIC_MAKEEXAMPLES } from '../../../modules/local/deepsomatic/makeexamples/main' +include { DEEPSOMATIC_CALLVARIANTS } from '../../../modules/local/deepsomatic/callvariants/main' +include { DEEPSOMATIC_POSTPROCESSVARIANTS } from '../../../modules/local/deepsomatic/postprocessvariants/main' workflow DEEPSOMATIC { take: diff --git a/subworkflows/local/dmr.nf b/subworkflows/local/dmr/main.nf similarity index 92% rename from subworkflows/local/dmr.nf rename to subworkflows/local/dmr/main.nf index 5d869c26..e7bea406 100644 --- a/subworkflows/local/dmr.nf +++ b/subworkflows/local/dmr/main.nf @@ -1,8 +1,8 @@ // IMPORT MODULES -include { HTSLIB_BGZIPTABIX } from '../../modules/nf-core/htslib/bgziptabix/main' -include { MODKIT_DMR } from '../../modules/nf-core/modkit/dmr/main' -include { DMR_HAPLOTYPE_REGIONS } from '../../modules/local/dmr/haplotype_regions/main' -include { DMR_NEAREST_GENE } from '../../modules/local/dmr/nearest_gene/main' +include { HTSLIB_BGZIPTABIX } from '../../../modules/nf-core/htslib/bgziptabix/main' +include { MODKIT_DMR } from '../../../modules/nf-core/modkit/dmr/main' +include { DMR_HAPLOTYPE_REGIONS } from '../../../modules/local/dmr/haplotype_regions/main' +include { DMR_NEAREST_GENE } from '../../../modules/local/dmr/nearest_gene/main' workflow DMR { diff --git a/subworkflows/local/ecdna.nf b/subworkflows/local/ecdna/main.nf similarity index 91% rename from subworkflows/local/ecdna.nf rename to subworkflows/local/ecdna/main.nf index 2c39d5af..02dcfbd2 100644 --- a/subworkflows/local/ecdna.nf +++ b/subworkflows/local/ecdna/main.nf @@ -3,12 +3,12 @@ // // IMPORT MODULES -include { ASCAT_TO_CORAL_BED } from '../../modules/local/ascattocoralbed/main' -include { CORAL_SEED } from '../../modules/local/coral/seed/main' -include { CORAL_RECONSTRUCT } from '../../modules/local/coral/reconstruct/main' -include { CORAL_CYCLE } from '../../modules/local/coral/cycle/main' -include { CORAL_PLOT } from '../../modules/local/coral/plot/main' -include { AMPLICONCLASSIFIER } from '../../modules/local/ampliconclassifier/main' +include { ASCAT_TO_CORAL_BED } from '../../../modules/local/ascattocoralbed/main' +include { CORAL_SEED } from '../../../modules/local/coral/seed/main' +include { CORAL_RECONSTRUCT } from '../../../modules/local/coral/reconstruct/main' +include { CORAL_CYCLE } from '../../../modules/local/coral/cycle/main' +include { CORAL_PLOT } from '../../../modules/local/coral/plot/main' +include { AMPLICONCLASSIFIER } from '../../../modules/local/ampliconclassifier/main' workflow ECDNA { diff --git a/subworkflows/local/fiberseq.nf b/subworkflows/local/fiberseq/main.nf similarity index 93% rename from subworkflows/local/fiberseq.nf rename to subworkflows/local/fiberseq/main.nf index abe94da8..0e5a8501 100644 --- a/subworkflows/local/fiberseq.nf +++ b/subworkflows/local/fiberseq/main.nf @@ -2,10 +2,10 @@ // Fiber-seq: m6A prediction (PacBio with kinetics), nucleosome and FIRE calling on the unaligned BAMs // -include { FIBERTOOLSRS_PREDICTM6A } from '../../modules/local/fibertoolsrs/predictm6a' -include { FIBERTOOLSRS_FIRE } from '../../modules/local/fibertoolsrs/fire' -include { FIBERTOOLSRS_NUCLEOSOMES } from '../../modules/local/fibertoolsrs/nucleosomes' -include { FIBERTOOLSRS_QC } from '../../modules/local/fibertoolsrs/qc' +include { FIBERTOOLSRS_PREDICTM6A } from '../../../modules/local/fibertoolsrs/predictm6a' +include { FIBERTOOLSRS_FIRE } from '../../../modules/local/fibertoolsrs/fire' +include { FIBERTOOLSRS_NUCLEOSOMES } from '../../../modules/local/fibertoolsrs/nucleosomes' +include { FIBERTOOLSRS_QC } from '../../../modules/local/fibertoolsrs/qc' workflow FIBERSEQ { diff --git a/subworkflows/local/padfoot_annotation.nf b/subworkflows/local/padfoot_annotation/main.nf similarity index 94% rename from subworkflows/local/padfoot_annotation.nf rename to subworkflows/local/padfoot_annotation/main.nf index 852d0a87..3cf487dc 100644 --- a/subworkflows/local/padfoot_annotation.nf +++ b/subworkflows/local/padfoot_annotation/main.nf @@ -1,6 +1,6 @@ // IMPORT MODULES -include { PADFOOT as PADFOOT_SEVERUS_WAKHAN } from '../../modules/local/padfoot/main' -include { PADFOOT as PADFOOT_SAVANA } from '../../modules/local/padfoot/main' +include { PADFOOT as PADFOOT_SEVERUS_WAKHAN } from '../../../modules/local/padfoot/main' +include { PADFOOT as PADFOOT_SAVANA } from '../../../modules/local/padfoot/main' // // Padfoot annotation of somatic SVs + CNAs, once per caller pair that produced output for a sample: diff --git a/subworkflows/local/paired/paired_smallvar_germline.nf b/subworkflows/local/paired/paired_smallvar_germline.nf index f1ba424d..f1dc9cb7 100644 --- a/subworkflows/local/paired/paired_smallvar_germline.nf +++ b/subworkflows/local/paired/paired_smallvar_germline.nf @@ -5,7 +5,7 @@ include { CLAIR3 } from '../../../modules/local/clair3/main.n // IMPORT SUBWORKFLOWS include { DEEPVARIANT } from '../../../subworkflows/nf-core/deepvariant/main.nf' -include { SMALL_VARIANT_CONSENSUS as GERMLINE_CONSENSUS } from '../../../subworkflows/local/small_variant_consensus.nf' +include { SMALL_VARIANT_CONSENSUS as GERMLINE_CONSENSUS } from '../../../subworkflows/local/small_variant_consensus/main.nf' workflow PAIRED_SMALLVAR_GERMLINE { diff --git a/subworkflows/local/paired/paired_smallvar_somatic.nf b/subworkflows/local/paired/paired_smallvar_somatic.nf index 5a499ec0..7bcf5258 100644 --- a/subworkflows/local/paired/paired_smallvar_somatic.nf +++ b/subworkflows/local/paired/paired_smallvar_somatic.nf @@ -6,8 +6,8 @@ include { BCFTOOLS_CONCAT } from '../../../modules/nf-core/bcftools/co include { BCFTOOLS_SORT } from '../../../modules/nf-core/bcftools/sort' // IMPORT SUBWORKFLOWS -include { DEEPSOMATIC } from '../../../subworkflows/local/deepsomatic.nf' -include { SMALL_VARIANT_CONSENSUS as SOMATIC_CONSENSUS } from '../../../subworkflows/local/small_variant_consensus.nf' +include { DEEPSOMATIC } from '../../../subworkflows/local/deepsomatic/main.nf' +include { SMALL_VARIANT_CONSENSUS as SOMATIC_CONSENSUS } from '../../../subworkflows/local/small_variant_consensus/main.nf' workflow PAIRED_SMALLVAR_SOMATIC { diff --git a/subworkflows/local/phasing_haplotyping.nf b/subworkflows/local/phasing_haplotyping/main.nf similarity index 95% rename from subworkflows/local/phasing_haplotyping.nf rename to subworkflows/local/phasing_haplotyping/main.nf index 9324a986..f974e510 100644 --- a/subworkflows/local/phasing_haplotyping.nf +++ b/subworkflows/local/phasing_haplotyping/main.nf @@ -1,22 +1,22 @@ // Import modules -include { LONGPHASE_PHASE as LONGPHASE_PHASE_GERMLINE } from '../../modules/nf-core/longphase/phase/main.nf' -include { LONGPHASE_PHASE as LONGPHASE_PHASE_SOMATIC } from '../../modules/nf-core/longphase/phase/main.nf' -include { LONGPHASE_HAPLOTAG } from '../../modules/nf-core/longphase/haplotag/main.nf' -include { LONGPHASE_MODCALL as LONGPHASE_MODCALL_GERMLINE } from '../../modules/local/longphase/modcall/main.nf' -include { LONGPHASE_MODCALL as LONGPHASE_MODCALL_SOMATIC } from '../../modules/local/longphase/modcall/main.nf' -include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main.nf' -include { BCFTOOLS_CONCAT } from '../../modules/nf-core/bcftools/concat/main' -include { BCFTOOLS_CONCAT as CONCAT_SOMATIC_UNPHASED } from '../../modules/nf-core/bcftools/concat/main' -include { BCFTOOLS_SORT } from '../../modules/nf-core/bcftools/sort/main' -include { BCFTOOLS_SORT as SORT_SOMATIC_PHASED } from '../../modules/nf-core/bcftools/sort/main' -include { BCFTOOLS_VIEW } from '../../modules/local/bcftools/view/main.nf' -include { BCFTOOLS_VIEW as SOMATIC_ALT } from '../../modules/local/bcftools/view/main.nf' -include { BCFTOOLS_VIEW as SOMATIC_NONALT } from '../../modules/local/bcftools/view/main.nf' -include { BCFTOOLS_EXCLUDE_SITES as GERMLINE_ANCHORS } from '../../modules/local/bcftools/excludesites/main.nf' -include { BCFTOOLS_NORM as REJOIN_SOMATIC } from '../../modules/nf-core/bcftools/norm/main' -include { BCFTOOLS_NORM as REJOIN_GERMLINE } from '../../modules/nf-core/bcftools/norm/main' -include { VCFTAG as TAG_SOMATIC } from '../../modules/local/vcftag/main.nf' -include { VCFTAG as TAG_GERMLINE } from '../../modules/local/vcftag/main.nf' +include { LONGPHASE_PHASE as LONGPHASE_PHASE_GERMLINE } from '../../../modules/nf-core/longphase/phase/main.nf' +include { LONGPHASE_PHASE as LONGPHASE_PHASE_SOMATIC } from '../../../modules/nf-core/longphase/phase/main.nf' +include { LONGPHASE_HAPLOTAG } from '../../../modules/nf-core/longphase/haplotag/main.nf' +include { LONGPHASE_MODCALL as LONGPHASE_MODCALL_GERMLINE } from '../../../modules/local/longphase/modcall/main.nf' +include { LONGPHASE_MODCALL as LONGPHASE_MODCALL_SOMATIC } from '../../../modules/local/longphase/modcall/main.nf' +include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main.nf' +include { BCFTOOLS_CONCAT } from '../../../modules/nf-core/bcftools/concat/main' +include { BCFTOOLS_CONCAT as CONCAT_SOMATIC_UNPHASED } from '../../../modules/nf-core/bcftools/concat/main' +include { BCFTOOLS_SORT } from '../../../modules/nf-core/bcftools/sort/main' +include { BCFTOOLS_SORT as SORT_SOMATIC_PHASED } from '../../../modules/nf-core/bcftools/sort/main' +include { BCFTOOLS_VIEW } from '../../../modules/local/bcftools/view/main.nf' +include { BCFTOOLS_VIEW as SOMATIC_ALT } from '../../../modules/local/bcftools/view/main.nf' +include { BCFTOOLS_VIEW as SOMATIC_NONALT } from '../../../modules/local/bcftools/view/main.nf' +include { BCFTOOLS_EXCLUDE_SITES as GERMLINE_ANCHORS } from '../../../modules/local/bcftools/excludesites/main.nf' +include { BCFTOOLS_NORM as REJOIN_SOMATIC } from '../../../modules/nf-core/bcftools/norm/main' +include { BCFTOOLS_NORM as REJOIN_GERMLINE } from '../../../modules/nf-core/bcftools/norm/main' +include { VCFTAG as TAG_SOMATIC } from '../../../modules/local/vcftag/main.nf' +include { VCFTAG as TAG_GERMLINE } from '../../../modules/local/vcftag/main.nf' workflow PHASING_HAPLOTYPING { diff --git a/subworkflows/local/prepare_aa_data_repo.nf b/subworkflows/local/prepare_aa_data_repo/main.nf similarity index 92% rename from subworkflows/local/prepare_aa_data_repo.nf rename to subworkflows/local/prepare_aa_data_repo/main.nf index 8d3cf924..84785063 100644 --- a/subworkflows/local/prepare_aa_data_repo.nf +++ b/subworkflows/local/prepare_aa_data_repo/main.nf @@ -2,8 +2,8 @@ // Stage the AmpliconArchitect data repository AmpliconClassifier reads at runtime // -include { AADATAREPO_DOWNLOAD } from '../../modules/local/aadatarepo/download/main' -include { UNTAR as UNTAR_AA_DATA_REPO } from '../../modules/nf-core/untar/main' +include { AADATAREPO_DOWNLOAD } from '../../../modules/local/aadatarepo/download/main' +include { UNTAR as UNTAR_AA_DATA_REPO } from '../../../modules/nf-core/untar/main' workflow PREPARE_AA_DATA_REPO { diff --git a/subworkflows/local/prepare_annotation.nf b/subworkflows/local/prepare_annotation/main.nf similarity index 96% rename from subworkflows/local/prepare_annotation.nf rename to subworkflows/local/prepare_annotation/main.nf index 114199a3..e5fe96a7 100644 --- a/subworkflows/local/prepare_annotation.nf +++ b/subworkflows/local/prepare_annotation/main.nf @@ -1,4 +1,4 @@ -include {ENSEMBLVEP_DOWNLOAD } from '../../modules/nf-core/ensemblvep/download/main.nf' +include {ENSEMBLVEP_DOWNLOAD } from '../../../modules/nf-core/ensemblvep/download/main.nf' workflow PREPARE_ANNOTATION { diff --git a/subworkflows/local/prepare_reference_files.nf b/subworkflows/local/prepare_reference_files/main.nf similarity index 93% rename from subworkflows/local/prepare_reference_files.nf rename to subworkflows/local/prepare_reference_files/main.nf index 3a105744..b5ef904e 100644 --- a/subworkflows/local/prepare_reference_files.nf +++ b/subworkflows/local/prepare_reference_files/main.nf @@ -2,13 +2,13 @@ // Prepare reference files (unzipping and adding index) // -include { PIGZ_UNCOMPRESS as UNZIP_FASTA } from '../../modules/nf-core/pigz/uncompress/main' -include { SAMTOOLS_FAIDX } from '../../modules/nf-core/samtools/faidx/main' -include { UNZIP as UNZIP_ALLELES } from '../../modules/nf-core/unzip/main' -include { UNZIP as UNZIP_GC } from '../../modules/nf-core/unzip/main' -include { UNZIP as UNZIP_LOCI } from '../../modules/nf-core/unzip/main' -include { UNZIP as UNZIP_RT } from '../../modules/nf-core/unzip/main' -include { CLAIR3_MODEL } from '../../modules/local/clair3_model/main' +include { PIGZ_UNCOMPRESS as UNZIP_FASTA } from '../../../modules/nf-core/pigz/uncompress/main' +include { SAMTOOLS_FAIDX } from '../../../modules/nf-core/samtools/faidx/main' +include { UNZIP as UNZIP_ALLELES } from '../../../modules/nf-core/unzip/main' +include { UNZIP as UNZIP_GC } from '../../../modules/nf-core/unzip/main' +include { UNZIP as UNZIP_LOCI } from '../../../modules/nf-core/unzip/main' +include { UNZIP as UNZIP_RT } from '../../../modules/nf-core/unzip/main' +include { CLAIR3_MODEL } from '../../../modules/local/clair3_model/main' workflow PREPARE_REFERENCE_FILES { take: diff --git a/subworkflows/local/prepare_signatures.nf b/subworkflows/local/prepare_signatures/main.nf similarity index 94% rename from subworkflows/local/prepare_signatures.nf rename to subworkflows/local/prepare_signatures/main.nf index 11cfc3d4..6209b6e1 100644 --- a/subworkflows/local/prepare_signatures.nf +++ b/subworkflows/local/prepare_signatures/main.nf @@ -1,5 +1,5 @@ -include { SIGPROFILER_INSTALL } from '../../modules/local/sigprofiler/install/main' -include { SIGPROFILER_VERIFY } from '../../modules/local/sigprofiler/verify/main' +include { SIGPROFILER_INSTALL } from '../../../modules/local/sigprofiler/install/main' +include { SIGPROFILER_VERIFY } from '../../../modules/local/sigprofiler/verify/main' workflow PREPARE_SIGNATURES { diff --git a/subworkflows/local/prepare_vep_plugins.nf b/subworkflows/local/prepare_vep_plugins/main.nf similarity index 86% rename from subworkflows/local/prepare_vep_plugins.nf rename to subworkflows/local/prepare_vep_plugins/main.nf index 0b8245d7..9dcfe6cd 100644 --- a/subworkflows/local/prepare_vep_plugins.nf +++ b/subworkflows/local/prepare_vep_plugins/main.nf @@ -3,13 +3,13 @@ // ClinVar once so the VEP tasks never stage it from its host themselves // -include { UNZIP as UNZIP_REVEL } from '../../modules/nf-core/unzip/main.nf' -include { UNZIP as UNZIP_EVE } from '../../modules/nf-core/unzip/main.nf' -include { WGET as WGET_REVEL } from '../../modules/nf-core/wget/main' -include { WGET as WGET_EVE } from '../../modules/nf-core/wget/main' -include { VEPPLUGIN_REVEL } from '../../modules/local/vepplugin/revel/main.nf' -include { VEPPLUGIN_EVE } from '../../modules/local/vepplugin/eve/main.nf' -include { VEPPLUGIN_CLINVAR } from '../../modules/local/vepplugin/clinvar/main.nf' +include { UNZIP as UNZIP_REVEL } from '../../../modules/nf-core/unzip/main.nf' +include { UNZIP as UNZIP_EVE } from '../../../modules/nf-core/unzip/main.nf' +include { WGET as WGET_REVEL } from '../../../modules/nf-core/wget/main' +include { WGET as WGET_EVE } from '../../../modules/nf-core/wget/main' +include { VEPPLUGIN_REVEL } from '../../../modules/local/vepplugin/revel/main.nf' +include { VEPPLUGIN_EVE } from '../../../modules/local/vepplugin/eve/main.nf' +include { VEPPLUGIN_CLINVAR } from '../../../modules/local/vepplugin/clinvar/main.nf' workflow PREPARE_VEP_PLUGINS { diff --git a/subworkflows/local/reconplot_figures.nf b/subworkflows/local/reconplot_figures/main.nf similarity index 94% rename from subworkflows/local/reconplot_figures.nf rename to subworkflows/local/reconplot_figures/main.nf index 0057a07d..cdb1575c 100644 --- a/subworkflows/local/reconplot_figures.nf +++ b/subworkflows/local/reconplot_figures/main.nf @@ -1,7 +1,7 @@ // IMPORT MODULES -include { RECONPLOT as RECONPLOT_SEVERUS_ASCAT } from '../../modules/local/reconplot/main' -include { RECONPLOT as RECONPLOT_SEVERUS_WAKHAN } from '../../modules/local/reconplot/main' -include { RECONPLOT as RECONPLOT_SAVANA } from '../../modules/local/reconplot/main' +include { RECONPLOT as RECONPLOT_SEVERUS_ASCAT } from '../../../modules/local/reconplot/main' +include { RECONPLOT as RECONPLOT_SEVERUS_WAKHAN } from '../../../modules/local/reconplot/main' +include { RECONPLOT as RECONPLOT_SAVANA } from '../../../modules/local/reconplot/main' // // ReConPlot rearrangement + copy-number figures for every CN/SV caller pair that produced output for diff --git a/subworkflows/local/small_variant_consensus.nf b/subworkflows/local/small_variant_consensus/main.nf similarity index 96% rename from subworkflows/local/small_variant_consensus.nf rename to subworkflows/local/small_variant_consensus/main.nf index 773609fd..83b7a712 100644 --- a/subworkflows/local/small_variant_consensus.nf +++ b/subworkflows/local/small_variant_consensus/main.nf @@ -1,11 +1,11 @@ -include { BCFTOOLS_NORM } from '../../modules/nf-core/bcftools/norm/main' -include { BCFTOOLS_NORM as BCFTOOLS_NORM_REJOIN } from '../../modules/nf-core/bcftools/norm/main' -include { BCFTOOLS_ISEC } from '../../modules/nf-core/bcftools/isec/main' -include { BCFTOOLS_QUERY } from '../../modules/nf-core/bcftools/query/main' -include { BCFTOOLS_ANNOTATE } from '../../modules/nf-core/bcftools/annotate/main' -include { BCFTOOLS_SORT as SORT_POST_NORM } from '../../modules/nf-core/bcftools/sort/main' -include { BCFTOOLS_SORT as BCFTOOLS_SORT_CONSENSUS } from '../../modules/nf-core/bcftools/sort/main' -include { BCFTOOLS_CALLER_UNION } from '../../modules/local/bcftools/callerunion/main' +include { BCFTOOLS_NORM } from '../../../modules/nf-core/bcftools/norm/main' +include { BCFTOOLS_NORM as BCFTOOLS_NORM_REJOIN } from '../../../modules/nf-core/bcftools/norm/main' +include { BCFTOOLS_ISEC } from '../../../modules/nf-core/bcftools/isec/main' +include { BCFTOOLS_QUERY } from '../../../modules/nf-core/bcftools/query/main' +include { BCFTOOLS_ANNOTATE } from '../../../modules/nf-core/bcftools/annotate/main' +include { BCFTOOLS_SORT as SORT_POST_NORM } from '../../../modules/nf-core/bcftools/sort/main' +include { BCFTOOLS_SORT as BCFTOOLS_SORT_CONSENSUS } from '../../../modules/nf-core/bcftools/sort/main' +include { BCFTOOLS_CALLER_UNION } from '../../../modules/local/bcftools/callerunion/main' diff --git a/subworkflows/local/tests/dmr.nf.test b/subworkflows/local/tests/dmr.nf.test index d8a88a05..a7c79909 100644 --- a/subworkflows/local/tests/dmr.nf.test +++ b/subworkflows/local/tests/dmr.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test Workflow DMR" - script "../dmr.nf" + script "../dmr/main.nf" workflow "DMR" config "./nextflow.config" diff --git a/subworkflows/local/tests/ecdna.nf.test b/subworkflows/local/tests/ecdna.nf.test index 0e7f8539..19bda0a6 100644 --- a/subworkflows/local/tests/ecdna.nf.test +++ b/subworkflows/local/tests/ecdna.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test Subworkflow ECDNA" - script "../ecdna.nf" + script "../ecdna/main.nf" workflow "ECDNA" tag "subworkflows" diff --git a/subworkflows/local/tests/padfoot_annotation.nf.test b/subworkflows/local/tests/padfoot_annotation.nf.test index 5d53a0ca..f6008088 100644 --- a/subworkflows/local/tests/padfoot_annotation.nf.test +++ b/subworkflows/local/tests/padfoot_annotation.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test Workflow PADFOOT_ANNOTATION" - script "../padfoot_annotation.nf" + script "../padfoot_annotation/main.nf" workflow "PADFOOT_ANNOTATION" tag "subworkflows" diff --git a/subworkflows/local/tests/prepare_aa_data_repo.nf.test b/subworkflows/local/tests/prepare_aa_data_repo.nf.test index c2910f67..5c45f98d 100644 --- a/subworkflows/local/tests/prepare_aa_data_repo.nf.test +++ b/subworkflows/local/tests/prepare_aa_data_repo.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test Subworkflow PREPARE_AA_DATA_REPO" - script "../prepare_aa_data_repo.nf" + script "../prepare_aa_data_repo/main.nf" workflow "PREPARE_AA_DATA_REPO" tag "subworkflows" diff --git a/subworkflows/local/tests/prepare_signatures.nf.test b/subworkflows/local/tests/prepare_signatures.nf.test index 3ea7f829..4e53a1b8 100644 --- a/subworkflows/local/tests/prepare_signatures.nf.test +++ b/subworkflows/local/tests/prepare_signatures.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test Workflow PREPARE_SIGNATURES" - script "../prepare_signatures.nf" + script "../prepare_signatures/main.nf" workflow "PREPARE_SIGNATURES" tag "subworkflows" diff --git a/subworkflows/local/tests/reconplot_figures.nf.test b/subworkflows/local/tests/reconplot_figures.nf.test index 2c9fbd3b..2217b559 100644 --- a/subworkflows/local/tests/reconplot_figures.nf.test +++ b/subworkflows/local/tests/reconplot_figures.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test Workflow RECONPLOT_FIGURES" - script "../reconplot_figures.nf" + script "../reconplot_figures/main.nf" workflow "RECONPLOT_FIGURES" tag "subworkflows" diff --git a/subworkflows/local/tumor_only/tumoronly_smallvar.nf b/subworkflows/local/tumor_only/tumoronly_smallvar.nf index 24c67719..b69d5a40 100644 --- a/subworkflows/local/tumor_only/tumoronly_smallvar.nf +++ b/subworkflows/local/tumor_only/tumoronly_smallvar.nf @@ -7,9 +7,9 @@ include { VCFSPLIT } from '../../../modules/local/vcfsplit/main // IMPORT SUBWORKFLOWS include { DEEPVARIANT } from '../../../subworkflows/nf-core/deepvariant/main.nf' -include { DEEPSOMATIC } from '../../../subworkflows/local/deepsomatic.nf' -include { SMALL_VARIANT_CONSENSUS as GERMLINE_CONSENSUS } from '../../../subworkflows/local/small_variant_consensus.nf' -include { SMALL_VARIANT_CONSENSUS as SOMATIC_CONSENSUS } from '../../../subworkflows/local/small_variant_consensus.nf' +include { DEEPSOMATIC } from '../../../subworkflows/local/deepsomatic/main.nf' +include { SMALL_VARIANT_CONSENSUS as GERMLINE_CONSENSUS } from '../../../subworkflows/local/small_variant_consensus/main.nf' +include { SMALL_VARIANT_CONSENSUS as SOMATIC_CONSENSUS } from '../../../subworkflows/local/small_variant_consensus/main.nf' // Germline verdict transfer: DeepSomatic adjudicates DeepVariant's tumor-derived germline calls. include { BCFTOOLS_NORM as DS_VERDICT_SPLIT_DS } from '../../../modules/nf-core/bcftools/norm/main' diff --git a/tests/chm13.nf.test.snap b/tests/chm13.nf.test.snap index 1e1877ae..fd474c86 100644 --- a/tests/chm13.nf.test.snap +++ b/tests/chm13.nf.test.snap @@ -159,7 +159,7 @@ "whatshap": 2.8 }, "Workflow": { - "IntGenomicsLab/lrsomatic": "v1.1.0" + "IntGenomicsLab/lrsomatic": "v1.2.0dev" } } ], diff --git a/tests/clair_only.nf.test.snap b/tests/clair_only.nf.test.snap index 9bff949b..a7762429 100644 --- a/tests/clair_only.nf.test.snap +++ b/tests/clair_only.nf.test.snap @@ -166,7 +166,7 @@ "whatshap": 2.8 }, "Workflow": { - "IntGenomicsLab/lrsomatic": "v1.1.0" + "IntGenomicsLab/lrsomatic": "v1.2.0dev" } }, [ diff --git a/tests/consensus.nf.test.snap b/tests/consensus.nf.test.snap index d641c78e..748289dd 100644 --- a/tests/consensus.nf.test.snap +++ b/tests/consensus.nf.test.snap @@ -210,7 +210,7 @@ "whatshap": 2.8 }, "Workflow": { - "IntGenomicsLab/lrsomatic": "v1.1.0" + "IntGenomicsLab/lrsomatic": "v1.2.0dev" } }, [ diff --git a/tests/deep_only.nf.test.snap b/tests/deep_only.nf.test.snap index 4a9f4862..235e658b 100644 --- a/tests/deep_only.nf.test.snap +++ b/tests/deep_only.nf.test.snap @@ -171,7 +171,7 @@ "whatshap": 2.8 }, "Workflow": { - "IntGenomicsLab/lrsomatic": "v1.1.0" + "IntGenomicsLab/lrsomatic": "v1.2.0dev" } }, [ diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 810824dd..72ffa7e8 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -147,7 +147,7 @@ "whatshap": 2.8 }, "Workflow": { - "IntGenomicsLab/lrsomatic": "v1.1.0" + "IntGenomicsLab/lrsomatic": "v1.2.0dev" } }, [ diff --git a/tests/nextflow.config b/tests/nextflow.config index 0ad47f65..fc33809d 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -4,8 +4,6 @@ ======================================================================================== */ -// TODO nf-core: Specify any additional parameters here -// Or any resources requirements params { modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/lrsomatic' diff --git a/tests/union.nf.test.snap b/tests/union.nf.test.snap index 274fbb7b..0602876a 100644 --- a/tests/union.nf.test.snap +++ b/tests/union.nf.test.snap @@ -204,7 +204,7 @@ "whatshap": 2.8 }, "Workflow": { - "IntGenomicsLab/lrsomatic": "v1.1.0" + "IntGenomicsLab/lrsomatic": "v1.2.0dev" } }, [ From d038cf94d18a138e1022e0a293cc0d4d17373250 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Thu, 29 Oct 2026 14:22:40 +0100 Subject: [PATCH 2/3] Fill in PR number in CHANGELOG entry Co-Authored-By: Claude Opus 5.5 --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6cf736d6..cdaf8702 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,7 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` -- [#PR](https://github.com/IntGenomicsLab/lrsomatic/pull/PR) - Cleared the pipeline-level nf-core lint warnings. `manifest.version` is now `1.2.0dev`; the 13 flat `subworkflows/local/*.nf` files moved to `subworkflows/local//main.nf`; `skip_modkit` is in the skip options group and six parameters got schema descriptions; template TODOs are resolved, including a pipeline citation in the MultiQC methods description and pipeline-specific contribution guidelines; and the stray `lint_log.txt` debug log is removed (@ljwharbers). +- [#227](https://github.com/IntGenomicsLab/lrsomatic/pull/227) - Cleared the pipeline-level nf-core lint warnings. `manifest.version` is now `1.2.0dev`; the 13 flat `subworkflows/local/*.nf` files moved to `subworkflows/local//main.nf`; `skip_modkit` is in the skip options group and six parameters got schema descriptions; template TODOs are resolved, including a pipeline citation in the MultiQC methods description and pipeline-specific contribution guidelines; and the stray `lint_log.txt` debug log is removed (@ljwharbers). - [#224](https://github.com/IntGenomicsLab/lrsomatic/pull/224) - Updated to the nf-core template for [nf-core/tools 4.2.1](https://github.com/nf-core/tools/releases/tag/4.2.1). Bumps nf-schema to 2.7.3 (needed for Nextflow 26.04) and nft-utils to 1.2.1, sets `manifest.diagram` to the existing metro map (`assets/lrsomatic_1.0.png`), replaces `fix_linting.yml` with the reusable `fix-linting.yml` from nf-core/actions, adds recommended VS Code extensions, and stops `workflow.onComplete` from blocking on the MultiQC report. The linting workflow keeps running plain `pre-commit` rather than the template's prek-action (@ljwharbers). - [#224](https://github.com/IntGenomicsLab/lrsomatic/pull/224) - Dropped `ext.use_gpu` from the GPU resource labels, following the template: `task.accelerator` now decides GPU use, and `CLAIR3` reads it instead of `task.ext.use_gpu` (@ljwharbers). - [#204](https://github.com/IntGenomicsLab/lrsomatic/pull/204) - With `--modkit_phased` set and haplotype DMR running, `5hmC` is appended to `--modified-bases` whenever `--modkit_args` names `5mC` without it, so the published `modkit_pileup/*_{hp1,hp2,combined}.bed.gz` now carry a 5hmC row next to each 5mC row. `modkit dmr pair` rejects bedMethyl rows whose valid coverage includes uncounted (`N_other`) calls, which ONT SUP data calling both 5mC and 5hmC produces under the `--cpg --modified-bases 5mC` default. Runs with `--skip_dmr`, without `--modkit_phased`, or without DMR references keep `--modkit_args` exactly as given (@YannVRB). From 8f0714a4a3335271011335a578ec6106a2ff6e03 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Mon, 2 Nov 2026 14:31:08 +0100 Subject: [PATCH 3/3] Address #227 review: boolean autocorrelation, version sync, extended list - autocorrelation is now a boolean defaulting to false (schema and nextflow.config), matching docs/usage.md. A bare --autocorrelation flag now validates, and --autocorrelation false no longer contradicts the description. - .nf-core.yml template.version 1.1.0 -> 1.2.0dev, matching manifest.version (version_consistency: "Version tags are consistent"). - CONTRIBUTING: refer to all tests tagged `extended` and list chm13. Co-Authored-By: Claude Opus 5.5 --- .nf-core.yml | 2 +- CHANGELOG.md | 2 +- docs/CONTRIBUTING.md | 2 +- nextflow.config | 2 +- nextflow_schema.json | 5 +++-- 5 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 80c387b7..f1bc5f3e 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -44,4 +44,4 @@ template: outdir: . skip_features: - fastqc - version: 1.1.0 + version: 1.2.0dev diff --git a/CHANGELOG.md b/CHANGELOG.md index cdaf8702..576c1250 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,7 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` -- [#227](https://github.com/IntGenomicsLab/lrsomatic/pull/227) - Cleared the pipeline-level nf-core lint warnings. `manifest.version` is now `1.2.0dev`; the 13 flat `subworkflows/local/*.nf` files moved to `subworkflows/local//main.nf`; `skip_modkit` is in the skip options group and six parameters got schema descriptions; template TODOs are resolved, including a pipeline citation in the MultiQC methods description and pipeline-specific contribution guidelines; and the stray `lint_log.txt` debug log is removed (@ljwharbers). +- [#227](https://github.com/IntGenomicsLab/lrsomatic/pull/227) - Cleared the pipeline-level nf-core lint warnings. `manifest.version` and the `.nf-core.yml` template version are now `1.2.0dev`; the 13 flat `subworkflows/local/*.nf` files moved to `subworkflows/local//main.nf`; `skip_modkit` is in the skip options group and six parameters got schema descriptions; `--autocorrelation` is now a boolean (default `false`), as `docs/usage.md` already described it, so a bare `--autocorrelation` flag passes validation; template TODOs are resolved, including a pipeline citation in the MultiQC methods description and pipeline-specific contribution guidelines; and the stray `lint_log.txt` debug log is removed (@ljwharbers). - [#224](https://github.com/IntGenomicsLab/lrsomatic/pull/224) - Updated to the nf-core template for [nf-core/tools 4.2.1](https://github.com/nf-core/tools/releases/tag/4.2.1). Bumps nf-schema to 2.7.3 (needed for Nextflow 26.04) and nft-utils to 1.2.1, sets `manifest.diagram` to the existing metro map (`assets/lrsomatic_1.0.png`), replaces `fix_linting.yml` with the reusable `fix-linting.yml` from nf-core/actions, adds recommended VS Code extensions, and stops `workflow.onComplete` from blocking on the MultiQC report. The linting workflow keeps running plain `pre-commit` rather than the template's prek-action (@ljwharbers). - [#224](https://github.com/IntGenomicsLab/lrsomatic/pull/224) - Dropped `ext.use_gpu` from the GPU resource labels, following the template: `task.accelerator` now decides GPU use, and `CLAIR3` reads it instead of `task.ext.use_gpu` (@ljwharbers). - [#204](https://github.com/IntGenomicsLab/lrsomatic/pull/204) - With `--modkit_phased` set and haplotype DMR running, `5hmC` is appended to `--modified-bases` whenever `--modkit_args` names `5mC` without it, so the published `modkit_pileup/*_{hp1,hp2,combined}.bed.gz` now carry a 5hmC row next to each 5mC row. `modkit dmr pair` rejects bedMethyl rows whose valid coverage includes uncounted (`N_other`) calls, which ONT SUP data calling both 5mC and 5hmC produces under the `--cpg --modified-bases 5mC` default. Runs with `--skip_dmr`, without `--modkit_phased`, or without DMR references keep `--modkit_args` exactly as given (@YannVRB). diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md index 97a76586..cd5eb2f8 100644 --- a/docs/CONTRIBUTING.md +++ b/docs/CONTRIBUTING.md @@ -166,4 +166,4 @@ If you update images or graphics, follow the nf-core [style guidelines](https:// - [ ] Keep the `[ meta, data ]` tuple shape across module and subworkflow boundaries, so sample metadata reaches every downstream step. - [ ] Put local subworkflows in `subworkflows/local//main.nf`. - [ ] Add a `CHANGELOG.md` entry with the PR number for every user-facing change. -- [ ] Tag fast (stub) tests with `small`: pull-request CI runs only tests with that tag. The extended pipeline tests (`clair_only`, `consensus`, `deep_only`, `union`) run only on release or manual dispatch, so regenerate their snapshots whenever an output changes. +- [ ] Tag fast (stub) tests with `small`: pull-request CI runs only tests with that tag. The extended pipeline tests (all tests tagged `extended`; currently `chm13`, `clair_only`, `consensus`, `deep_only` and `union`) run only on release or manual dispatch, so regenerate their snapshots whenever an output changes. diff --git a/nextflow.config b/nextflow.config index adc6b318..e0c36209 100644 --- a/nextflow.config +++ b/nextflow.config @@ -128,7 +128,7 @@ params { save_secondary_alignment = true // Fibertools options - autocorrelation = null + autocorrelation = false // Severus options severus_minsupport = 3 diff --git a/nextflow_schema.json b/nextflow_schema.json index 893a4690..a3955b6c 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -225,8 +225,9 @@ "default": "", "properties": { "autocorrelation": { - "type": "string", - "description": "Pass --acf to fibertools qc to add the nucleosome autocorrelation to the Fiber-seq QC output. Any non-empty value turns it on." + "type": "boolean", + "default": false, + "description": "Pass --acf to fibertools qc to add nucleosome autocorrelation to the Fiber-seq QC output." } } },