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Add prokka protein #239

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Merged
lpantano merged 9 commits into from
May 16, 2025
Merged

Add prokka protein #239

lpantano merged 9 commits into from
May 16, 2025

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@lpantano lpantano commented May 14, 2025 •
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Accept a protein fasta file to be used by prokka for custom annotation.
Clean subworkflow warning to follow nf-core recommendation

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/bacass branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines 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 14, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 459435f

+| ✅ 215 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!
Details

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.1
  • Run at 2025-05-16 13:45:55

@lpantano lpantano marked this pull request as ready for review May 14, 2025 18:41
@lpantano lpantano requested review from Daniel-VM and d4straub May 14, 2025 19:37
d4straub
d4straub approved these changes May 15, 2025
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LGTM
The CHANGELOG (1) could have its entry adapted to the other though, i.e. adding the PR link, and (2) could mention the exact new parameter.

@lpantano lpantano merged commit e51f39e into dev May 16, 2025
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@lpantano lpantano deleted the add_prokka_protein branch May 16, 2025 20:19
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@d4straub d4straub d4straub approved these changes

@Daniel-VM Daniel-VM Awaiting requested review from Daniel-VM

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