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Added test_nothing nf-test and updated CI #620

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Added test_nothing nf-test and updated CI #620

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CarsonJM
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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/mag 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 May 23, 2024 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f1dddfe

+| ✅ 307 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • 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:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-13 17:52:27

@prototaxites
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Not knowing much (yet) about nf-test - I think this looks great!

I had a poke around in the failing tests - here, the kreport test fails because the test reads the mag conf/modules.conf and sets the prefix as ext.prefix = { "${meta.id}_kreport" }, whereas the test snapshot expects the output file to just be called ${meta.id}.txt. I suspect this could be a problem for any test where we're manually setting a prefix and adding custom strings to it which aren't hard-coded in the process itself. Off the top of my head this may cause problems with the read QC filtering, phiX removal, etc. as these add prefixes like "_host_removed" to separate out fastq files which otherwise would have the same names.

@CarsonJM
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Thanks for taking a look at this @prototaxites! I'll look at the module configs today and see which ones need to be changed, I think this is something we can override in an nf-test config 👌

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@CarsonJM @prototaxites @jfy133