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Update trimming subworkflow to include more tests #1271

Merged
merged 2 commits into from
Mar 22, 2024
Merged

Update trimming subworkflow to include more tests #1271

merged 2 commits into from
Mar 22, 2024

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adamrtalbot
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@adamrtalbot adamrtalbot commented Mar 19, 2024 •
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Update trimming subworkflow to include more tests.

Closes #1267
Contributes to #1195

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).

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github-actions bot commented Mar 19, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2179ef9

+| ✅ 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 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!
  • 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

❔ 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 2024-03-19 17:52:18

pinin4fjords
pinin4fjords reviewed Mar 19, 2024
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subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap Outdated
"single_end": false
},
[
"/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz",
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Not sure how this ended up the snapshot, or which output it is (since the individual output snapshots aren't named), but maybe we need to fix in modules?

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It's on skip_trimming, you can see the title just above. Maybe the channel is passed transparently to the output and so it passes the path directly?

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@adamrtalbot adamrtalbot Mar 19, 2024 •
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Wait, skip trimming skips everything in the subworkflow.

Let's just remove it as an option!

Wrong, wasn't scrolling up.

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@adamrtalbot adamrtalbot Mar 19, 2024 •
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Fixed in nf-core/modules#5278. Will update once merged.

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askimed/nf-test#205

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Merged now, let's see what happens...

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Success!

@adamrtalbot adamrtalbot merged commit 1817d14 into nf-core:dev Mar 22, 2024
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@adamrtalbot adamrtalbot mentioned this pull request Apr 4, 2024
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@pinin4fjords pinin4fjords pinin4fjords approved these changes

@drpatelh drpatelh Awaiting requested review from drpatelh

@maxulysse maxulysse Awaiting requested review from maxulysse

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@adamrtalbot @pinin4fjords