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Gens replace local module#785

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peterpru merged 12 commits into
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gens-replace-local-module
Mar 16, 2026
Merged

Gens replace local module#785
peterpru merged 12 commits into
devfrom
gens-replace-local-module

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@peterpru peterpru commented Mar 13, 2026 •
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This PR replaces the local gens modules with the nf-core gens version, to make this tools easier to maintain.

For the reviewer: the nf-core module generates tbi index files, so we can remove the extra tabix indexing steps in the subworkflow.

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/raredisease branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Ensure the test suite passes (nextflow run . -profile test_singleton,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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nf-core-bot commented Mar 13, 2026

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions Bot commented Mar 13, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 96d7d64

+| ✅ 234 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   8 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ mq_metrics = SENTIEON_DATAMETRICS.out.mq_metrics.ifEmpty(null) // channel: [ val(meta), path(mq_metrics) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ qd_metrics = SENTIEON_DATAMETRICS.out.qd_metrics.ifEmpty(null) // channel: [ val(meta), path(qd_metrics) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ gc_metrics = SENTIEON_DATAMETRICS.out.gc_metrics.ifEmpty(null) // channel: [ val(meta), path(gc_metrics) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ gc_summary = SENTIEON_DATAMETRICS.out.gc_summary.ifEmpty(null) // channel: [ val(meta), path(gc_summary) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ aln_metrics = SENTIEON_DATAMETRICS.out.aln_metrics.ifEmpty(null) // channel: [ val(meta), path(aln_metrics) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ is_metrics = SENTIEON_DATAMETRICS.out.is_metrics.ifEmpty(null) // channel: [ val(meta), path(is_metrics) ]
    _
  • schema_lint - Input mimetype is missing or empty
  • schema_description - No description provided in schema for parameter: hisat2

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-03-16 14:07:15

@peterpru peterpru self-assigned this Mar 16, 2026
@peterpru peterpru marked this pull request as ready for review March 16, 2026 10:18
fellen31
fellen31 reviewed Mar 16, 2026
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Comment thread subworkflows/local/gens/main.nf Outdated
@peterpru @fellen31
Update subworkflows/local/gens/main.nf
fdd0040 
Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>
@peterpru peterpru requested a review from fellen31 March 16, 2026 13:16
fellen31
fellen31 reviewed Mar 16, 2026
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Nice! Could you also remove the local gens module and add the version changes in the "Tool updates" section of the Changelog?

I don't see any pipeline test snapshot changes (which would help verify that the versions have changed and are captured). Looks like we're skipping gens there, not sure why, should be fully possible.

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peterpru commented Mar 16, 2026

Nice! Could you also remove the local gens module and add the version changes in the "Tool updates" section of the Changelog?

I don't see any pipeline test snapshot changes (which would help verify that the versions have changed and are captured). Looks like we're skipping gens there, not sure why, should be fully possible.

Thanks. I have now deleted the local module and updated the Tools section in the changelog. I see you made an issue for the pipeline test, I will leave that out of this PR.

fellen31
fellen31 reviewed Mar 16, 2026
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Update CHANGELOG.md
96d7d64 
Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>
fellen31
fellen31 approved these changes Mar 16, 2026
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LGTM!

@peterpru peterpru merged commit b566760 into dev Mar 16, 2026
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@peterpru peterpru mentioned this pull request Mar 18, 2026
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@ramprasadn ramprasadn deleted the gens-replace-local-module branch March 30, 2026 20:58
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@fellen31 fellen31 fellen31 approved these changes

@sofiademmou sofiademmou Awaiting requested review from sofiademmou

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