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More tests for subworkflows #713

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PR checklist

This PR

  1. Adds tests for call_repeat_exapansions and qc_bam subworkflows
  2. Updates modules included in the above subworkflows
  • 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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github-actions bot commented Jul 10, 2025 •
edited
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 986f6ad

+| ✅ 221 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗  21 tests had warnings |!

❗ Test warnings:

  • pipeline_if_empty_null - ifEmpty(null) found in 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 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 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 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 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 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
  • local_component_structure - annotate_mt_snvs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - subsample_mt.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - generate_clinical_set.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - generate_cytosure_files.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - annotate_structural_variants.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - annotate_genome_snvs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - annotate_consequence_pli.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - gens.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - call_mobile_elements.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - rank_variants.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - variant_evaluation.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - call_structural_variants.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - annotate_mobile_elements.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - call_snv.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ 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 3.3.2
  • Run at 2025-07-10 21:06:51

@ramprasadn ramprasadn marked this pull request as ready for review July 11, 2025 11:54
fellen31
fellen31 reviewed Jul 14, 2025
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Nice, thanks for keeping it shorter!

Missing changelog.

conf/modules/qc_bam.config
@@ -55,6 +55,7 @@ process {
}

withName: '.*QC_BAM:MOSDEPTH' {
ext.args = "--d4"
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👍

subworkflows/local/call_repeat_expansions/tests/main.nf.test
then {
assert workflow.success
assert snapshot(
path(workflow.out.vcf[0][1].toString()).vcf.variantsMD5
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I like to have vcf.summary here as well, but nothing required.

subworkflows/local/qc_bam/tests/main.nf.test
params {
aligner = "bwamem2"
skip_tools = null
outdir = "tests/results"
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Suggested change
outdir = "tests/results"

Same here?

subworkflows/local/call_repeat_expansions/tests/main.nf.test
Comment on lines +13 to +15
params {
outdir = "tests/results"
}
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Suggested change
params {
outdir = "tests/results"
}

Why do you need this?

subworkflows/local/qc_bam/tests/main.nf.test
params {
aligner = "sentieon"
skip_tools = null
outdir = "tests/results"
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Suggested change
outdir = "tests/results"

subworkflows/local/qc_bam/tests/nextflow.config
Comment on lines +38 to +39
// NGSBITS_SAMPLEGENDER needs a chrX and chrY in order to run so we skip it for the two test profiles
ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_singleton', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun }
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Could consider adding a stub test where you run this process.

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@ramprasadn @fellen31