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Add option to specify call for manta#867

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ramprasadn merged 9 commits into
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caddfix
Jun 3, 2026
Merged

Add option to specify call for manta#867
ramprasadn merged 9 commits into
patchfrom
caddfix

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@ramprasadn ramprasadn commented Jun 1, 2026

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 Jun 1, 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 Jun 1, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit aa58f16

+| ✅ 243 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   9 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.0.0
  • 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 2026-06-03 09:53:37

@ramprasadn ramprasadn marked this pull request as ready for review June 1, 2026 12:46
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ramprasadn commented Jun 1, 2026

@nf-core-bot fix linting

fellen31
fellen31 requested changes Jun 1, 2026
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@fellen31 fellen31 left a comment

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Nice! Some comments on the implementation, but looks good overall 👍

Comment thread main.nf Outdated
Comment thread subworkflows/local/call_sv_manta/main.nf
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@fellen31 fellen31 Jun 1, 2026

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Seems like ch_bed and ch_manta_call_regions serve the same purpose in this subworkflow. Could you add upstream logic to either supply the wes target bed file or the manta call regions to this subworkflow instead to reduce the duplication?

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@fellen31 fellen31 Jun 2, 2026

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Did you have a look at this comment @ramprasadn?

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@ramprasadn ramprasadn Jun 3, 2026

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Yes, I did. Its been addressed now.

Comment thread subworkflows/local/call_structural_variants/main.nf
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@fellen31 fellen31 Jun 1, 2026

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Same as https://github.com/nf-core/raredisease/pull/867/changes#r3334612426.

Comment thread CHANGELOG.md
@ramprasadn ramprasadn requested a review from fellen31 June 2, 2026 07:13
fellen31
fellen31 approved these changes Jun 3, 2026
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Good solution!

@ramprasadn ramprasadn merged commit b425008 into patch Jun 3, 2026
47 of 48 checks passed
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@fellen31 fellen31 fellen31 approved these changes

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