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add pipeline level tests #1661

Merged
merged 12 commits into from
Oct 1, 2024
Merged

add pipeline level tests #1661

merged 12 commits into from
Oct 1, 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/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).

@maxulysse
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following nf-core/rnaseq#1379, trying it out in sarek

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github-actions bot commented Sep 19, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c1ab3de

+| ✅ 201 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 2024-10-01 08:38:54

nvnieuwk
nvnieuwk approved these changes Oct 1, 2024
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LOVE IT!

@maxulysse maxulysse merged commit 6e7655f into nf-core:dev Oct 1, 2024
30 checks passed
@maxulysse maxulysse deleted the pipeline_test branch October 1, 2024 09:18
FriederikeHanssen
FriederikeHanssen reviewed Oct 1, 2024
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tests/main.nf.test.snap
Comment on lines +46 to +50
"csv",
"markduplicates.csv",
"markduplicates_no_table.csv",
"recalibrated.csv",
"variantcalled.csv",
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why are these not stable?

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because they contain the full path and not the relative one, I need to sort this out

FriederikeHanssen
FriederikeHanssen reviewed Oct 1, 2024
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tests/main.nf.test.snap
"reports",
"bcftools",
"strelka",
"test",
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why are folder names showing up several times here?

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so it's actually like a tree arborescence but flat, so any duplicate name is actually in a different location

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@FriederikeHanssen FriederikeHanssen FriederikeHanssen left review comments

@nvnieuwk nvnieuwk nvnieuwk approved these changes

@sateeshperi sateeshperi sateeshperi approved these changes

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4 participants
@maxulysse @FriederikeHanssen @sateeshperi @nvnieuwk