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FEAT: remove old profile tests that are not used anymore in CI #2084

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Merged
FriederikeHanssen merged 19 commits into from
Jan 13, 2026
Merged

FEAT: remove old profile tests that are not used anymore in CI #2084

FriederikeHanssen merged 19 commits into from
Jan 13, 2026
+1,745 −644

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@maxulysse
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@maxulysse maxulysse commented Dec 17, 2025

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 pipelines 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 Dec 17, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 19955a7

+| ✅ 224 tests passed       |+
#| ❔  13 tests were ignored |#
!| ❗   7 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • 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!
  • schema_lint - Input mimetype is missing or empty
  • schema_description - No description provided in schema for parameter: markduplicates_pixel_distance
  • schema_description - No description provided in schema for parameter: gatk_pcr_indel_model

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-01-12 14:12:24

FriederikeHanssen
FriederikeHanssen reviewed Dec 17, 2025
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FriederikeHanssen
FriederikeHanssen requested changes Dec 17, 2025
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while you are at it: the fastp tests still contain references to additional profiles. Spark is referenceing an extra profile in the call. test_tools_manually also has some references left

maxulysse
maxulysse commented Dec 17, 2025
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maxulysse
maxulysse commented Dec 17, 2025
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maxulysse
maxulysse commented Dec 17, 2025
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FriederikeHanssen commented Jan 12, 2026

Changelog Please!!!

FriederikeHanssen
FriederikeHanssen reviewed Jan 12, 2026
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tests/variant_calling_all.nf.test
name: "-profile test --input tests/csv/3.0/fastq_pair.csv --tools cnvkit,deepvariant,freebayes,mpileup,msisensorpro,strelka,tiddit",
params: [
input: "${projectDir}/tests/csv/3.0/fastq_pair.csv",
tools: "cnvkit,deepvariant,freebayes,mpileup,msisensorpro,strelka,tiddit"
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not important for now, but let's enhance by reviewing the tools. I think lofreq and msisensor2, muse are missing

@FriederikeHanssen FriederikeHanssen mentioned this pull request Jan 12, 2026
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@FriederikeHanssen FriederikeHanssen merged commit fe1bfb7 into dev Jan 13, 2026
74 of 79 checks passed
@FriederikeHanssen FriederikeHanssen deleted the tests_cleanup_config branch January 13, 2026 15:35
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@heuermh heuermh heuermh approved these changes

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@maxulysse @FriederikeHanssen @heuermh