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Fix match check of assembly and sample IDs#648

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prototaxites merged 6 commits intonf-core:devfrom
prototaxites:fix_match
Aug 6, 2024
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Fix match check of assembly and sample IDs#648
prototaxites merged 6 commits intonf-core:devfrom
prototaxites:fix_match

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@prototaxites prototaxites commented Aug 2, 2024 •
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Fixes #647

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 Aug 2, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3b509ed

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

❗ 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 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 2024-08-06 09:35:22

jfy133
jfy133 approved these changes Aug 6, 2024
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Small documentation improvements, but otherwise LGTM, thanks again @prototaxites !

Conceptually tested in nf-console with:

workflow {
  ch_a = Channel.of("a", "b", "c").toList()
  ch_b = Channel.of("d", "e", "f").toList()
  
  // fails as cross returns nothing
  ch_a.cross(ch_b)
  .map { ids1, ids2 ->
    if (ids1.sort() != ids2.sort()) {
      log.warn( "[nf-core/mag] ERROR: supplied IDs or Groups in read and assembly CSV files do not match!")
      }
    }

  // returns list of lists so the check runs and fails
  ch_a.concat(ch_b).collect(flat: false)
  .view()
  .map { ids1, ids2 ->
    if (ids1.sort() != ids2.sort()) {
      log.warn("[nf-core/mag] ERROR: supplied IDs or Groups in read and assembly CSV files do not match!")
      }
    }
}```

Comment thread CHANGELOG.md Outdated
Comment thread subworkflows/local/utils_nfcore_mag_pipeline/main.nf Outdated
Comment thread CHANGELOG.md Outdated
prototaxites and others added 3 commits August 6, 2024 10:32
@prototaxites @jfy133
Update CHANGELOG.md
f143707 
Co-authored-by: James A. Fellows Yates <[email protected]>
@prototaxites @jfy133
Update subworkflows/local/utils_nfcore_mag_pipeline/main.nf
098c192 
Co-authored-by: James A. Fellows Yates <[email protected]>
@prototaxites @jfy133
Update CHANGELOG.md
3b509ed 
Co-authored-by: James A. Fellows Yates <[email protected]>
@prototaxites prototaxites merged commit 6ebc119 into nf-core:dev Aug 6, 2024
@prototaxites prototaxites mentioned this pull request Aug 6, 2024
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@prototaxites prototaxites deleted the fix_match branch August 7, 2024 10:36
@jfy133 jfy133 mentioned this pull request Aug 22, 2024
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@jfy133 jfy133 mentioned this pull request Oct 2, 2024
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