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Fix centrifuge#618

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jfy133 merged 8 commits intodevfrom
fix-centrifuge
May 23, 2024
Merged

Fix centrifuge#618
jfy133 merged 8 commits intodevfrom
fix-centrifuge

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@jfy133 jfy133 commented May 16, 2024 •
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Closes #597

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 16, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b44e0f5

+| ✅ 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 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 2024-05-23 12:41:39

@jfy133 jfy133 marked this pull request as draft May 16, 2024 12:29
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jfy133 commented May 16, 2024 •
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TODO:

  • CLean up output in results directory to match in docs
  • Remove dumps
  • Check CI fails above

But otherwise look slike output is expected now

@jfy133 jfy133 marked this pull request as ready for review May 23, 2024 11:54
@jfy133 jfy133 requested a review from skrakau May 23, 2024 11:55
prototaxites
prototaxites reviewed May 23, 2024
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jfy133 commented May 23, 2024
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@jfy133 jfy133 requested a review from prototaxites May 23, 2024 12:39
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Couple small comments - otherwise LGTM! (but don't have the latitude to test it myself right now)

@jfy133 jfy133 merged commit 333caeb into dev May 23, 2024
@jfy133 jfy133 deleted the fix-centrifuge branch May 23, 2024 15:21
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@prototaxites prototaxites prototaxites approved these changes

@skrakau skrakau Awaiting requested review from skrakau

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