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Update CI from rnaseq, strip unused rnaseq components #45

Merged
merged 8 commits into from
Apr 11, 2024
Merged

Update CI from rnaseq, strip unused rnaseq components #45

merged 8 commits into from
Apr 11, 2024

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pinin4fjords
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@pinin4fjords pinin4fjords commented Apr 10, 2024 •
edited

In this PR:

  • Update the nf-test-driven CI inherited from nf-core/rnaseq
  • Remove config and other things related to components not copied over from nf-core/rnaseq.

Some of these components (e.g. post-alignment QC steps) may well be useful here too. They should be 'factored out' of nf-core/rnaseq as subworkflows and added later, but removing their footprint for now.

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/riboseq 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 Apr 10, 2024 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b1fd885

+| ✅ 178 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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!
  • schema_description - No description provided in schema for parameter: skip_ribotricer

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-11 10:33:53

@pinin4fjords pinin4fjords changed the title Misc fixes Update CI from rnaseq, strip unused nf-core/rnaseq components Apr 10, 2024
@pinin4fjords pinin4fjords changed the title Update CI from rnaseq, strip unused nf-core/rnaseq components Update CI from rnaseq, strip unused rnaseq components Apr 10, 2024
jfy133
jfy133 approved these changes Apr 11, 2024
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Don't see anything funky 👍

main.nf Outdated Show resolved Hide resolved
@pinin4fjords pinin4fjords merged commit a4a64e3 into dev Apr 11, 2024
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@pinin4fjords pinin4fjords deleted the misc_fixes branch April 11, 2024 10:32
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@jfy133 jfy133 jfy133 approved these changes

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