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Fix RRNATRANSCRIPT bug not detecting input gtf #564

Merged
merged 6 commits into from
Dec 3, 2024
Merged

Fix RRNATRANSCRIPT bug not detecting input gtf #564

merged 6 commits into from
Dec 3, 2024

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atrigila
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@atrigila atrigila commented Dec 2, 2024 •
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Closes #563

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/rnafusion branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • 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).

@atrigila atrigila self-assigned this Dec 2, 2024
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github-actions bot commented Dec 2, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9602378

+| ✅ 220 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-12-03 17:51:36

@atrigila atrigila requested a review from rannick December 2, 2024 16:03
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atrigila commented Dec 2, 2024

Let's fix this upsteam in nf-core/modules

@atrigila atrigila requested a review from alanmmobbs93 December 2, 2024 18:18
nschcolnicov
nschcolnicov approved these changes Dec 3, 2024
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👍

@atrigila atrigila merged commit 489161e into nf-core:dev Dec 3, 2024
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@nschcolnicov nschcolnicov nschcolnicov approved these changes

@rannick rannick Awaiting requested review from rannick

@alanmmobbs93 alanmmobbs93 Awaiting requested review from alanmmobbs93

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@atrigila @alanmmobbs93 @nschcolnicov