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Fix strintie io #416

Merged
merged 9 commits into from
Oct 2, 2023
Merged

Fix strintie io #416

merged 9 commits into from
Oct 2, 2023

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rannick
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@rannick rannick commented Oct 2, 2023 •
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Closes #415 and adds stringtie to github ci tests

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!
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

@rannick rannick mentioned this pull request Oct 2, 2023
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github-actions bot commented Oct 2, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8ece842

+| ✅ 158 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • pipeline_todos - TODO string in WorkflowRnafusion.groovy: Optionally add in-text citation tools to this list.

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-02 11:26:02

@rannick rannick self-assigned this Oct 2, 2023
@rannick rannick added the WIP Work in progress label Oct 2, 2023
@rannick rannick requested review from fevac and peterpru October 2, 2023 11:28
@rannick rannick removed the WIP Work in progress label Oct 2, 2023
fevac
fevac approved these changes Oct 2, 2023
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Nice! 🌟

.github/workflows/ci.yml
@@ -104,3 +104,10 @@ jobs:
--outdir /home/runner/work/rnafusion/rnafusion/results --starfusion \
--genomes_base /home/runner/work/rnafusion/rnafusion/results/references \
--cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }}

- name: Dry test stingtie
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let's revisit the ci in a future PR

@rannick rannick merged commit 91a5927 into dev Oct 2, 2023
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@rannick rannick deleted the fix_strintie_io branch November 27, 2023 15:54
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@fevac fevac fevac approved these changes

@peterpru peterpru Awaiting requested review from peterpru

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Not a valid path value type: java.util.LinkedHashMap ([id:Homo_sapiens.GRCh38.102.chr.gtf])
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