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Adress issues from review #469

Merged
merged 31 commits into from
Oct 14, 2024
Merged

Adress issues from review #469

merged 31 commits into from
Oct 14, 2024

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apeltzer
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@apeltzer apeltzer commented Oct 8, 2024

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/smrnaseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • 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).

@apeltzer apeltzer added this to the 2.4.0 milestone Oct 8, 2024
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github-actions bot commented Oct 8, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5254dae

+| ✅ 243 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.fastp_known_mirna_adapters

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-13 21:17:40

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apeltzer commented Oct 8, 2024

@nf-core-bot fix linting

@atrigila atrigila mentioned this pull request Oct 8, 2024
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atrigila commented Oct 8, 2024

I can't reproduce the error:

CI:
image
Gitpod:
image

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apeltzer commented Oct 8, 2024

CI not working now because of the template v.3.0.0 release. I'm afraid we need to merge thta one in too :-(

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Likely Need to merge in 3.0.1 First and then work on this

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Mergen in dev with Template Channels so that wie can fix anything remaining here and then push everything to dev. Hopefully that should do the Trick and we‘re there then .)

@apeltzer
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Issue with template will be fixed today with nf-core/tools 3.0.2 —> we should merge that in here directly then.

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Ok next steps would be merging #474 to this PR's branch. Then merging this one to dev and ultimately then making the release after updating the changelog date appropriately :)

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⚠️ Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.1.
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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Ok should be fine to go

maxulysse
maxulysse reviewed Oct 14, 2024
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maxulysse
maxulysse approved these changes Oct 14, 2024
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@apeltzer apeltzer merged commit 4ca8cb1 into dev Oct 14, 2024
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mashehu
mashehu approved these changes Oct 14, 2024
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@apeltzer apeltzer deleted the adress-issues branch October 14, 2024 08:52
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@maxulysse maxulysse maxulysse approved these changes

@mashehu mashehu mashehu approved these changes

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@apeltzer @atrigila @nf-core-bot @maxulysse @mashehu @nschcolnicov