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Strip problematic ifEmpty() #1317

Merged
merged 2 commits into from
Jun 12, 2024
Merged

Strip problematic ifEmpty() #1317

merged 2 commits into from
Jun 12, 2024

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pinin4fjords
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@pinin4fjords pinin4fjords commented Jun 12, 2024 •
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Currently, if CAT_FASTQ doesn't fire, rnaseq will error like:

Cannot invoke "java.nio.file.Path.getFileSystem()" because "path" is null

This is because of this line:

ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null))

Because CAT_FASTQ does not fire (as in test_full), ch_versions gets a null emission, which gets passed to softwareVersionsToYAML() and thence to processVersionsFromYAML(), which attempts to read the null as a file and triggers the getFileSystem() error.

As far as I can tell the ifEmpty() is a hangover of a bygone era, so I propose we just strip it.

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 Jun 12, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a8eb811

+| ✅ 171 tests passed       |+
#| ❔   9 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:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-12 16:27:32

@pinin4fjords pinin4fjords merged commit e277e3e into dev Jun 12, 2024
185 checks passed
@ewels ewels deleted the strip_ifempty branch June 12, 2024 19:37
@pinin4fjords pinin4fjords mentioned this pull request Jul 19, 2024
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@pinin4fjords pinin4fjords mentioned this pull request Oct 15, 2024
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@maxulysse maxulysse maxulysse approved these changes

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