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Add dedicated optitype output folder. #170

Merged
merged 2 commits into from
Aug 5, 2024
Merged

Add dedicated optitype output folder. #170

merged 2 commits into from
Aug 5, 2024

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SpikyClip
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Description

Currently, the results of optitype get stored in the params.outdir folder (i.e. results) by sample, alongside other tool outputs (e.g. multiqc, fastqc, pipeline_info). It would be neater if it were stored by default in the folder ${params.outdir}/optitype. While this is a sort of a subjective decision, it would be necessary if other tools were added in the future, to distinguish the tools output. It can still be overridden if needed by the users custom configs.

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/hlatyping 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).

@SpikyClip SpikyClip requested a review from jonasscheid July 29, 2024 05:55
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github-actions bot commented Jul 29, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 654df5b

+| ✅ 182 tests passed       |+
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • 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 passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-02 10:54:15

christopher-mohr
christopher-mohr approved these changes Jul 29, 2024
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Also LGTM, linting fails due to the template changes as mentioned in the other PR.

@christopher-mohr
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Hi @SpikyClip, the template merge is done. Could you please merge dev in your branch to make linting happy? :)

@christopher-mohr christopher-mohr merged commit e1390ed into nf-core:dev Aug 5, 2024
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@christopher-mohr christopher-mohr christopher-mohr approved these changes

@jonasscheid jonasscheid jonasscheid approved these changes

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@SpikyClip @christopher-mohr @jonasscheid