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add nf-tests for star_align_igenomes #1233

Merged
merged 2 commits into from
Mar 7, 2024
Merged

add nf-tests for star_align_igenomes #1233

merged 2 commits into from
Mar 7, 2024

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maxulysse
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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/rnaseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,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).

@maxulysse maxulysse mentioned this pull request Mar 5, 2024
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github-actions bot commented Mar 5, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 66848be

+| ✅ 169 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • nextflow_config - Config default ignored: params.ribo_database_manifest
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
  • multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-05 13:06:35

ramprasadn
ramprasadn reviewed Mar 6, 2024
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modules/local/star_align_igenomes/main.nf
@@ -8,20 +8,20 @@ process STAR_ALIGN_IGENOMES {
'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }"

input:
tuple val(meta), path(reads)
tuple val(meta), path(reads, stageAs: "input*/*")
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Why do you need stageAs here?

modules/local/star_align_igenomes/main.nf
tuple val(meta), path('*Log.final.out') , emit: log_final
tuple val(meta), path('*Log.out') , emit: log_out
tuple val(meta), path('*Log.progress.out'), emit: log_progress
path "versions.yml" , emit: versions

tuple val(meta), path('*d.out.bam') , optional:true, emit: bam
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Is this channel supposed to be a superset of bam_sorted channel?

@maxulysse
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@ramprasadn I copied the whole logic from the star align module, we need another local version to deal with older indexes in igenomes

@ramprasadn
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Cool! I'm a little puzzled by the choice of the *d.out.bam pattern to populate the bam channel, considering it could potentially clash with the *sortedByCoord.out.bam pattern used for the bam_sorted channel. However, since this line was added nearly a year ago and hasn't posed any problems yet, I'll just overlook it.

ramprasadn
ramprasadn approved these changes Mar 6, 2024
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LGTM!

@maxulysse maxulysse merged commit e50665a into nf-core:dev Mar 7, 2024
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@adamrtalbot adamrtalbot mentioned this pull request Mar 11, 2024
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@ramprasadn ramprasadn ramprasadn approved these changes

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@maxulysse @ramprasadn