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fix logical gate: when stringtie and not starfusion, only alignment i… #482

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merged 4 commits into from Apr 3, 2024
Merged

fix logical gate: when stringtie and not starfusion, only alignment i… #482

merged 4 commits into from Apr 3, 2024

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rannick
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@rannick rannick commented Apr 3, 2024 •
edited

fix logical gate:
When stringtie should have run, but not starfusion, starfusion ran anyways

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).
  • Ensure the test suite passes (nextflow run . -profile 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 Apr 3, 2024 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 88a3540

+| ✅ 167 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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:

  • 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 2.13.1
  • Run at 2024-04-03 12:19:16

@rannick rannick self-assigned this Apr 3, 2024
peterpru
peterpru approved these changes Apr 3, 2024
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Looks good to me 👍

@rannick rannick merged commit e50eed2 into dev Apr 3, 2024
6 checks passed
@rannick rannick deleted the fix_stringtie_log_gate branch April 3, 2024 14:03
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@peterpru peterpru peterpru approved these changes

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