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Fix genomeAttribute usage #1252

Merged
merged 11 commits into from
Apr 22, 2024
Merged

Fix genomeAttribute usage #1252

merged 11 commits into from
Apr 22, 2024

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maxulysse
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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/rnaseq 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 Mar 11, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 17767e1

+| ✅ 167 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • 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
  • 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: conf/modules.config
  • nextflow_config - Config default ignored: params.ribo_database_manifest
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
  • multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-12 15:56:41

drpatelh
drpatelh reviewed Mar 11, 2024
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@adamrtalbot
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@maxulysse is this still valid?

adamrtalbot
adamrtalbot approved these changes Apr 12, 2024
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I don't think this is that bad. I think it's readable and the parameter stuff is kept separate from the pipeline stuff (where it should be). We need a better solution but we wont have that until we can dedicate real time to the genomes.

@maxulysse maxulysse mentioned this pull request Apr 12, 2024
Merged
10 tasks
@maxulysse maxulysse merged commit b67141d into nf-core:dev Apr 22, 2024
184 checks passed
@maxulysse maxulysse deleted the getGenomeAttribute branch April 22, 2024 14:00
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@ramprasadn ramprasadn ramprasadn left review comments

@drpatelh drpatelh drpatelh left review comments

@adamrtalbot adamrtalbot adamrtalbot approved these changes

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@maxulysse @adamrtalbot @ramprasadn @drpatelh