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Published 20 hours ago • verified publisher icon nf-core

Add new testing strategy based on nf-test files

Open adamrtalbot opened this issue 11 months ago • 2 comments

Changes:

  • Workflow now parses repo for changed files with Python
  • Runs relevant tests by listing their nf-test files as the matrix of values
  • Uses tags to check for dependencies only

Related to: https://github.com/nf-core/phageannotator/pull/97 https://github.com/nf-core/fetchngs/pull/300

PR checklist

  • [x] This comment contains a description of changes (with reason).
  • [x] If you've fixed a bug or added code that should be tested, add tests!
  • [x] 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).
  • [x] 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.
  • [x] CHANGELOG.md is updated.
  • [ ] README.md is updated (including new tool citations and authors/contributors).

adamrtalbot avatar Mar 11 '24 11:03 adamrtalbot

nf-core lint overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit f244455

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

:heavy_exclamation_mark: 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!

:grey_question: 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

:white_check_mark: Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-09 12:24:59

github-actions[bot] avatar Mar 11 '24 11:03 github-actions[bot]

This snippet should fix the linting with the actions_ci https://github.com/nf-core/fetchngs/blob/8ec2d934f9301c818d961b1e4fdf7fc79610bdc5/.nf-core.yml#L2-L3

drpatelh avatar Mar 12 '24 10:03 drpatelh