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Include nf-tests for rsem_merge_counts module #1249

Merged
merged 10 commits into from
Mar 12, 2024
Merged

Include nf-tests for rsem_merge_counts module #1249

merged 10 commits into from
Mar 12, 2024

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robsyme
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@robsyme robsyme commented Mar 9, 2024 •
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Overview

This is a first attempt at converting the testing for the rsem_merge_counts local module to nf-test. It includes very small test data checked in with the workflow. I'm following the standard I've seen in other modules such as deseq2_qc.

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).

@robsyme robsyme changed the base branch from master to dev March 9, 2024 22:18
@nf-core nf-core deleted a comment from github-actions bot Mar 9, 2024
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github-actions bot commented Mar 9, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 49d8fff

+| ✅ 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 2024-03-12 11:17:35

@robsyme robsyme mentioned this pull request Mar 9, 2024
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@robsyme robsyme marked this pull request as ready for review March 9, 2024 22:45
adamrtalbot
adamrtalbot approved these changes Mar 9, 2024
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Minor things but theory is sound.

modules/local/rsem_merge_counts/tests/main.nf.test Outdated Show resolved Hide resolved
modules/local/rsem_merge_counts/tests/main.nf.test Outdated Show resolved Hide resolved
@maxulysse
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I don't like having the files here... really they should go in the the test-dataset repo on the rnaseq branch

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adamrtalbot commented Mar 11, 2024 •
edited by drpatelh
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Will close #1170

@adamrtalbot adamrtalbot linked an issue Mar 11, 2024 that may be closed by this pull request
Add nf-test to RSEM_MERGE_COUNTS module #1170
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@adamrtalbot adamrtalbot merged commit 2e315c1 into dev Mar 12, 2024
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@adamrtalbot adamrtalbot deleted the nftest_rsem_merge_counts branch March 12, 2024 11:30
@adamrtalbot adamrtalbot mentioned this pull request Mar 14, 2024
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@adamrtalbot adamrtalbot adamrtalbot approved these changes

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Add nf-test to RSEM_MERGE_COUNTS module
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@robsyme @maxulysse @adamrtalbot