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Improve read renaming #93

Merged
merged 3 commits into from
May 28, 2024
Merged

Improve read renaming #93

merged 3 commits into from
May 28, 2024

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fbdtemme
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Remove the RENAME_READS module. Replace the functionality by creating symlinks in PIXELATOR_AMPLICON.
This saves bandwidth and time on remote executors.

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/pixelator 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 28, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6407896

+| ✅ 201 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.2.0
  • 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 2024-05-28 08:04:18

@fbdtemme fbdtemme requested a review from johandahlberg May 28, 2024 08:14
johandahlberg
johandahlberg approved these changes May 28, 2024
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Super!

@fbdtemme fbdtemme merged commit 7e470cc into nf-core:dev May 28, 2024
4 checks passed
@fbdtemme fbdtemme deleted the improve-read-renaming branch May 29, 2024 15:30
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@johandahlberg johandahlberg johandahlberg approved these changes

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@fbdtemme @johandahlberg