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Fix the multiple fastq outputs in LONGREAD_HOSTREMOVAL #430

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Merged
merged 4 commits into from
Jan 23, 2024
Merged

Fix the multiple fastq outputs in LONGREAD_HOSTREMOVAL #430

merged 4 commits into from
Jan 23, 2024

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LilyAnderssonLee
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Close the issue #429

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/taxprofiler 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 Jan 22, 2024 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 28c850f

+| ✅ 164 tests passed       |+

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-22 17:31:22

@LilyAnderssonLee LilyAnderssonLee requested review from jfy133, sofstam and a team and removed request for jfy133 and sofstam January 22, 2024 12:09
sofstam
sofstam approved these changes Jan 22, 2024
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conf/modules.config Outdated
path: { "${params.outdir}/samtools/fastq" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
pattern: '*.unmapped_other.fastq.gz',
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Suggested change
pattern: '*.unmapped_other.fastq.gz',
pattern: '*._other.fastq.gz',

Maybe use the same pattern as in the module

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Thanks. I will change it into *_other.fastq.gz

@sofstam sofstam self-requested a review January 22, 2024 16:33
@LilyAnderssonLee LilyAnderssonLee merged commit 1f34a9a into dev Jan 23, 2024
@LilyAnderssonLee LilyAnderssonLee deleted the samtools_fastq branch January 23, 2024 10:10
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@sofstam sofstam Awaiting requested review from sofstam sofstam is a code owner

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@LilyAnderssonLee @sofstam