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Add nf-test to local module STARFUSION_DETECT #586

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merged 12 commits into from
Dec 20, 2024
Merged

Add nf-test to local module STARFUSION_DETECT #586

merged 12 commits into from
Dec 20, 2024

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atrigila
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@atrigila atrigila commented Dec 16, 2024 •
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Closes #585.

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).

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Dec 16, 2024 •
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nf-core pipelines lint overall result: Passed ✅

Posted for pipeline commit 945bf0f

+| ✅ 222 tests passed       |+
#| ❔   2 tests were ignored |#

❔ 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 2024-12-20 14:09:35

@atrigila atrigila self-assigned this Dec 16, 2024
@atrigila atrigila mentioned this pull request Dec 18, 2024
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@atrigila atrigila marked this pull request as ready for review December 19, 2024 19:18
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As discussed, this test covers a unit test when fastq files are provided as input. In order to make it more comprehensive, a test case will be added in the future that covers when the Chimeric.out.junction file is used as input: #593

@atrigila atrigila requested a review from rannick December 19, 2024 19:33
rannick
rannick approved these changes Dec 20, 2024
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atrigila and others added 3 commits December 20, 2024 11:07
@atrigila @rannick
Update modules/local/starfusion/detect/main.nf
ed4855e 
Co-authored-by: Annick Renevey <47788523+rannick@users.noreply.github.com>
@atrigila @rannick
Update modules/local/starfusion/detect/main.nf
f42d9dc 
Co-authored-by: Annick Renevey <47788523+rannick@users.noreply.github.com>
@atrigila
Merge branch 'dev' into starfusion_detect
945bf0f
@atrigila atrigila merged commit a815895 into nf-core:dev Dec 20, 2024
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@atrigila atrigila mentioned this pull request Dec 20, 2024
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@rannick rannick rannick approved these changes

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