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Add nf-tests for deseq2_qc local module #1241

Merged
merged 3 commits into from
Mar 7, 2024
Merged

Add nf-tests for deseq2_qc local module #1241

merged 3 commits into from
Mar 7, 2024

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adamrtalbot
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@adamrtalbot adamrtalbot commented Mar 7, 2024 •
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  • Generate test data on the fly to make everything faster and not rely on external dependencies.
  • Runs basic tests for success.

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).

@adamrtalbot adamrtalbot mentioned this pull request Mar 7, 2024
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github-actions bot commented Mar 7, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ff2ddbc

+| ✅ 169 tests passed       |+
#| ❔   8 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 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ 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_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 2024-03-07 12:43:05

@pinin4fjords
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pinin4fjords commented Mar 7, 2024 •
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Not a fan of extensive content in tests like this, I prefer separation of concerns and I think this is really hard to read.

@adamrtalbot
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Not a fan of extensive content in tests like this, I prefer separation of concerns and I think this is really hard to read.

Moved to separate files.

@adamrtalbot adamrtalbot merged commit 704212b into nf-core:dev Mar 7, 2024
28 checks passed
@adamrtalbot adamrtalbot deleted the nf-test_deseq2qc branch March 7, 2024 13:50
@adamrtalbot adamrtalbot mentioned this pull request Mar 11, 2024
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@maxulysse maxulysse maxulysse approved these changes

@pinin4fjords pinin4fjords Awaiting requested review from pinin4fjords

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@adamrtalbot @pinin4fjords @maxulysse