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Update nextclade & pangolin modules #446

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Update nextclade & pangolin modules #446

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Joon-Klaps
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@Joon-Klaps Joon-Klaps commented Nov 5, 2024 •
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PR checklist

Nextclade & pangolin modules are getting outdated and were requested to be updated.

  • 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/viralrecon 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 Nov 5, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b88cdcf

+| ✅ 201 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • 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
  • system_exit - System.exit in nanopore.nf: System.exit(1) [line 246]

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-05 09:02:19

@Joon-Klaps
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I'm trying to find when the --reference option for nextclade dataset get was removed. However, I've not been able to find it (yet). I therefore decided to remove the param --nextclade_dataset_reference which was the argument that got passed to --reference.

This was referenced Nov 5, 2024
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@Joon-Klaps Joon-Klaps marked this pull request as ready for review November 5, 2024 12:10
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@svarona svarona Awaiting requested review from svarona

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