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Cleanup output #156

Merged
merged 16 commits into from
Aug 12, 2024
Merged

Cleanup output #156

merged 16 commits into from
Aug 12, 2024

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edmundmiller
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@edmundmiller edmundmiller commented Aug 5, 2024 •
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Closes #89

Reworks the published directory and cuts down on the actual published files.

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/nascent 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>).
  • 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).

@edmundmiller edmundmiller added this to the 2.3.0 milestone Aug 5, 2024
@edmundmiller edmundmiller self-assigned this Aug 5, 2024
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github-actions bot commented Aug 5, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ebeb042

+| ✅ 199 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • 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

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • actions_ci - actions_ci

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-12 02:54:31

@edmundmiller edmundmiller marked this pull request as ready for review August 6, 2024 17:40
@edmundmiller edmundmiller force-pushed the cleanup-output branch 3 times, most recently from 4026329 to 26b6716 Compare August 10, 2024 19:50
@edmundmiller edmundmiller merged commit b35668b into dev Aug 12, 2024
7 checks passed
@edmundmiller edmundmiller deleted the cleanup-output branch August 12, 2024 18:22
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@nvnieuwk nvnieuwk nvnieuwk approved these changes

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