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Fix ref build #420

Merged
merged 5 commits into from
Oct 20, 2023
Merged

Fix ref build #420

merged 5 commits into from
Oct 20, 2023

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rannick
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@rannick rannick commented Oct 18, 2023 •
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Here as small fixes that were affecting building references:

  • fusionreport cosmic database was outdated -> updated to 2.1.5p5
  • the check for existence of the samplesheet was removed. As one usually build references without providing a samplesheet, this was causing an error
  • removing a REFORMAT config in modules.conf that was still there even thought the harsh trimming was removed

Local tests pass.

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 Oct 18, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fffb37b

+| ✅ 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 2023-10-20 08:30:07

@rannick rannick self-assigned this Oct 18, 2023
@rannick rannick requested a review from fevac October 20, 2023 08:35
peterpru
peterpru approved these changes Oct 20, 2023
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LGTM! 👍

@rannick rannick merged commit cf845e1 into dev Oct 20, 2023
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@rannick rannick deleted the fix_ref_build branch October 20, 2023 08:44
fevac
fevac approved these changes Oct 20, 2023
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🚀

@rannick rannick mentioned this pull request Oct 20, 2023
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@peterpru peterpru peterpru approved these changes

@fevac fevac fevac approved these changes

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