robert-a-forsyth · Nov 3, 2026 · Oct 29, 2026 · Oct 29, 2026 · Nov 2, 2026 · Nov 2, 2026
diff --git 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
@@ -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/<name>/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
@@ -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))
 
-<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
-     workflows use the "tube map" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->
-
 ## Usage
 
 > [!NOTE]

diff --git 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 '${workflow}' object
 data: |
   <h4>Methods</h4>
-  <p>Data was processed using IntGenomicsLab/lrsomatic v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
+  <p>Data was processed using IntGenomicsLab/lrsomatic v${workflow.manifest.version} ${doi_text} (<a href="https://doi.org/10.64898/2026.02.26.707772">Forsyth, Harbers <em>et al.</em>, 2026</a>), built with the nf-core framework (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
   <p>The pipeline was executed with Nextflow v${workflow.nextflow.version} (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p>
   <pre><code>${workflow.commandLine}</code></pre>
   <p>${tool_citations}</p>
   <h4>References</h4>
   <ul>
+    <li>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: <a href="https://doi.org/10.64898/2026.02.26.707772">10.64898/2026.02.26.707772</a></li>
     <li>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: <a href="https://doi.org/10.1038/nbt.3820">10.1038/nbt.3820</a></li>
     <li>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: <a href="https://doi.org/10.1038/s41587-020-0439-x">10.1038/s41587-020-0439-x</a></li>
     <li>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: <a href="https://doi.org/10.1038/s41592-018-0046-7">10.1038/s41592-018-0046-7</a></li>

diff --git 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
@@ -162,4 +162,8 @@ If you update images or graphics, follow the nf-core [style guidelines](https://
 
 ## Pipeline specific contribution guidelines
 
-<!-- TODO nf-core: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc. -->
+- [ ] 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/<name>/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 (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.