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Add an option to skip multiallelics split step in SNV calling workflows.#823

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ramprasadn merged 6 commits into
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bcftools_norm
Apr 27, 2026
Merged

Add an option to skip multiallelics split step in SNV calling workflows.#823
ramprasadn merged 6 commits into
devfrom
bcftools_norm

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@ramprasadn

@ramprasadn ramprasadn commented Apr 27, 2026

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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).

@nf-core-bot

nf-core-bot commented Apr 27, 2026

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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.

@github-actions

github-actions Bot commented Apr 27, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d771f2f

+| ✅ 244 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 2026-04-27 12:55:11

@ramprasadn

ramprasadn commented Apr 27, 2026

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@nf-core fix linting

@ramprasadn ramprasadn requested a review from ktruve April 27, 2026 12:49
@ramprasadn ramprasadn marked this pull request as ready for review April 27, 2026 12:49
@ramprasadn ramprasadn mentioned this pull request Apr 27, 2026
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@ramprasadn ramprasadn changed the title Add an otpion to skip multiallelics split step in SNV calling workflows. Add an option to skip multiallelics split step in SNV calling workflows. Apr 27, 2026
@ramprasadn ramprasadn merged commit a68931d into dev Apr 27, 2026
46 of 47 checks passed
@ramprasadn ramprasadn deleted the bcftools_norm branch April 27, 2026 15:10
@ktruve

ktruve commented Apr 27, 2026

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Well @jemten I checked out the PR #823 that @ramprasadn asked me to review. I saw now that you already merged that, but the errors are there. The CNVnator issue is already reported #817 and I just wanted to pinpoint that it is still there in this PR. It seem to be a known container issue that may vary across operating systems. For now we commented it out.

@ramprasadn

ramprasadn commented Apr 27, 2026

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Hi @ktruve, thanks for taking a look, and sorry for the confusion around the merge. I was trying to get these changes in quickly while starting the analysis for the final set of release branch validation cases, so I pulled in an additional reviewer to help move things along.

Just to clarify on the CNVnator issue, I initially thought it had been resolved on your end as well. From our discussion today, it seems it’s still present, although it’s working on our side. So it likely needs some deeper, environment-specific investigation.

Once we get the release out next week, I’ll make time to sync up with your colleagues so we can dig into it together and pinpoint the root cause.

Thanks again for flagging it! And sorry again for the confusion.

ktruve pushed a commit to ClinicalGenomicsGBG/nf-core-raredisease that referenced this pull request Apr 28, 2026
refactor: remove normalize_multiallelics param (covered by upstream PR …
0f26315 
…nf-core#823)
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@jemten jemten jemten approved these changes

@ktruve ktruve Awaiting requested review from ktruve

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@ramprasadn @nf-core-bot @ktruve @jemten