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Migrate pipeline pytest alignment and annotation tests to nf-test #1708

Merged
merged 11 commits into from
Oct 29, 2024
Merged

Migrate pipeline pytest alignment and annotation tests to nf-test #1708

merged 11 commits into from
Oct 29, 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).

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github-actions bot commented Oct 29, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d745104

+| ✅ 215 tests passed       |+
#| ❔  11 tests were ignored |#
!| ❗   4 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!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-29 10:05:18

@maxulysse maxulysse changed the title convert tests Migrate pipeline pytest alignment and annotation tests to nf-test Oct 29, 2024
FriederikeHanssen
FriederikeHanssen reviewed Oct 29, 2024
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tests/alignment_from_everything.nf.test
tag "pipeline_sarek"
profile "alignment_from_everything"

test("Run with profile test,alignment_from_everything | --save_mapped --save_output_as_bam") {
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can we name this better

FriederikeHanssen
FriederikeHanssen reviewed Oct 29, 2024
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tests/annotation_merge.nf.test
@@ -39,16 +40,17 @@ nextflow_pipeline {
}
}

test("Run with profile test | --tools vep --vep_include_fasta") {
test("Run with profile test | --tools merge,snpeff,vep") {
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looking at this we need to be more careful with the tool naming now that vcf merging (and not annotation merging) is coming cc @Patricie34

@maxulysse maxulysse enabled auto-merge (squash) October 29, 2024 10:42
@maxulysse maxulysse merged commit 65935d2 into nf-core:dev Oct 29, 2024
36 checks passed
@maxulysse maxulysse deleted the pytest_convert branch October 29, 2024 11:21
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@maxulysse @FriederikeHanssen