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 5a5b86b1..3d9717c0 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` +- [#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. `CLAIR3` now reads `params.use_gpu` instead of `task.ext.use_gpu`, the same param that picks its label and container, as DeepVariant, DeepSomatic and fibertools already do (@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