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merging template updates v3.0.2 #785

Merged
merged 14 commits into from
Oct 21, 2024
Merged

merging template updates v3.0.2 #785

merged 14 commits into from
Oct 21, 2024

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d4straub
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@d4straub d4straub commented Oct 18, 2024 •
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Template update 3.0.2

Testing with conda is excluded, because several profiles do not work with conda. It would be interesting though if there is a nice way to run some test profiles with conda and some without.

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/ampliseq 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).

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github-actions bot commented Oct 18, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ce6684f

+| ✅ 296 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • 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 ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-21 13:43:53

@d4straub
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@nf-core-bot fix linting

@d4straub
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test fails because the reference taxonomy database via dada_ref_taxonomy = "gtdb=R07-RS207" seems to be not reachable at the moment, i.e. https://data.ace.uq.edu.au/public/gtdb/data/releases/ doesnt work.
Will wait a little. Other options might be sbdi-gtdb=R06-RS202-3 which is at https://scilifelab.figshare.com or rdp=18 that links to zenodo.

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erikrikarddaniel commented Oct 21, 2024 •
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Earlier, we had some problems with the main site for GTDB that I think are solved now. You could update the config to use paths here: https://data.gtdb.ecogenomic.org/releases/release207/207.0/ (This is the main site.)

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Great thanks, trying that out!

@d4straub d4straub marked this pull request as ready for review October 21, 2024 13:17
mashehu
mashehu approved these changes Oct 21, 2024
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previous indentation was correct, error in the template

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Thanks, I'll go back to the original indentation!

@d4straub d4straub merged commit 0ac3093 into nf-core:dev Oct 21, 2024
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@d4straub d4straub deleted the merging-template-updates_3.0.2 branch October 21, 2024 19:50
@d4straub d4straub mentioned this pull request Oct 22, 2024
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@mashehu mashehu mashehu approved these changes

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@d4straub @erikrikarddaniel @mashehu @nf-core-bot