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Retire snpeff_genome #1656

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merged 9 commits into from
Sep 23, 2024
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asp8200
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@asp8200 asp8200 commented Sep 18, 2024

Retiring snpeff_genome. Instead using snpeff_db as ${snpeff_genome}.${snpeff_db} was previously used.

Reason: #1654
https://nfcore.slack.com/archives/C05V9FRJYMV/p1726589176199069

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/sarek 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 Sep 18, 2024

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9e3356a

+| ✅ 200 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • 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:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-19 14:25:52

@asp8200 asp8200 changed the title Retiring snpeff_genome Retire snpeff_genome Sep 18, 2024
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@maxulysse
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Looking good, we'd need to do these changes upstream in modules, and once that's done, I'll update annotation cache to make it work with that too

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asp8200 commented Sep 19, 2024

Looking good, we'd need to do these changes upstream in modules, and once that's done, I'll update annotation cache to make it work with that too

Yes, I'll update the modules over in the nf-core/modules-repo.

@asp8200 asp8200 marked this pull request as ready for review September 19, 2024 14:28
@asp8200 asp8200 requested a review from maxulysse September 20, 2024 07:02
@maxulysse maxulysse merged commit a4f07f7 into nf-core:dev Sep 23, 2024
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