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Add tests for subworkflows -II#782

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ramprasadn merged 18 commits into
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updatesubwfs1
Mar 10, 2026
Merged

Add tests for subworkflows -II#782
ramprasadn merged 18 commits into
devfrom
updatesubwfs1

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@ramprasadn ramprasadn commented Mar 5, 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).

@ramprasadn ramprasadn changed the title Updatesubwfs1 Add tests for subworkflows -II Mar 5, 2026
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nf-core-bot commented Mar 5, 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 5, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9c44193

+| ✅ 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 2026-03-10 12:26:09

@ramprasadn ramprasadn marked this pull request as ready for review March 5, 2026 15:04
fellen31
fellen31 reviewed Mar 6, 2026
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Cool!

Comment thread subworkflows/local/annotate_cadd/tests/main.nf.test.snap
Comment on lines +3 to +18
"content": [
{
"0": [

],
"1": [

],
"tbi": [

],
"vcf": [

]
}
],
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@fellen31 fellen31 Mar 6, 2026

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Looks empty. Is this intended?

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@ramprasadn ramprasadn Mar 9, 2026

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Good catch! Fixed

Comment thread subworkflows/local/annotate_cadd/tests/nextflow.config

withName: 'CADD' {
container = "nf-core/ubuntu:22.04" //Using an basic container because v1.7.3 is too big for CI.
ext.args = { "-g ${params.genome}" }
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I don't see params.genome in the main.nf.test

Comment thread subworkflows/local/annotate_cadd/main.nf Outdated
.join(TABIX_CADD.out.index)
.set { ch_annotate_in }

BCFTOOLS_ANNOTATE(ch_annotate_in, [], ch_header.map { _meta, header -> header }, ch_rename_chrs)
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Saw they changed the inputs in the latest nf-core module.

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@ramprasadn ramprasadn Mar 9, 2026

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Updated the module and related workflows

Comment thread subworkflows/local/annotate_genome_snvs/tests/main.nf.test
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@fellen31 fellen31 Mar 6, 2026

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Should be possible with a real test here, right? Except for cadd.

Comment thread subworkflows/local/annotate_mobile_elements/tests/nextflow.config
Comment thread subworkflows/local/rank_variants/tests/main.nf.test
Comment thread CHANGELOG.md
@ramprasadn ramprasadn requested a review from fellen31 March 9, 2026 14:17
fellen31
fellen31 requested changes Mar 10, 2026
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Comment thread subworkflows/local/call_snv_sentieon/main.nf Outdated
Comment on lines +102 to +104
.map { it -> it + [[]] }
.combine(ch_foundin_header)
.map { it -> it + [[]] }
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I would use something more verbose than it.

Comment thread subworkflows/local/call_snv_sentieon/main.nf Outdated

BCFTOOLS_MERGE(ch_vcf_idx_merge_in.multiple, ch_genome_fasta, ch_genome_fai, [[:],[]])
BCFTOOLS_MERGE(
ch_vcf_idx_merge_in.multiple.map { it -> it + [[]] },
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Same here.

Comment thread subworkflows/local/call_snv_deepvariant/main.nf Outdated
Comment on lines +75 to +77
.map { it -> it + [[]] }
.combine(ch_foundin_header)
.map { it -> it + [[]] }
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@fellen31 fellen31 Mar 10, 2026

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And here.

fellen31
fellen31 reviewed Mar 10, 2026
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Comment thread subworkflows/local/postprocess_MT_calls/main.nf Outdated
[[:],[]]
BCFTOOLS_MERGE_MT(
ch_case_vcf.multiple.map { it -> it + [[]] },
ch_genome_fasta.join(ch_genome_fai, failOnMismatch:true, failOnDuplicate:true)
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Do you only run this process once, or do you need a .collect() after the join?

fellen31
fellen31 reviewed Mar 10, 2026
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Comment thread subworkflows/local/call_snv_sentieon/main.nf Outdated
BCFTOOLS_MERGE(ch_vcf_idx_merge_in.multiple, ch_genome_fasta, ch_genome_fai, [[:],[]])
BCFTOOLS_MERGE(
ch_vcf_idx_merge_in.multiple.map { it -> it + [[]] },
ch_genome_fasta.join(ch_genome_fai, failOnMismatch:true, failOnDuplicate:true)
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@fellen31 fellen31 Mar 10, 2026

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Do you only run this process one, or do you need a .collect() after the join?

fellen31
fellen31 approved these changes Mar 10, 2026
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Nice, if you could change the last its as well that would be great.

Comment thread subworkflows/local/postprocess_MT_calls/main.nf Outdated
Comment on lines +115 to +117
.map { it -> it + [[]] }
.combine(ch_foundin_header)
.map { it -> it + [[]] }
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Perhaps you could change these its as well.

Comment thread subworkflows/local/postprocess_MT_calls/main.nf Outdated
ch_genome_fai,
[[:],[]]
BCFTOOLS_MERGE_MT(
ch_case_vcf.multiple.map { it -> it + [[]] },
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And this it.

@ramprasadn ramprasadn merged commit e406c03 into dev Mar 10, 2026
34 checks passed
@ramprasadn ramprasadn deleted the updatesubwfs1 branch March 30, 2026 18:47
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