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Add nf-test for test_minimal#686

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sofstam wants to merge 1 commit intodevfrom
add_test_minimal
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Add nf-test for test_minimal#686
sofstam wants to merge 1 commit intodevfrom
add_test_minimal

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@sofstam sofstam commented Feb 12, 2026

This PR adds nf-test for test_minimal profile

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/taxprofiler 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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nf-core-bot commented Feb 12, 2026

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Feb 12, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 04b5533

+| ✅ 293 tests passed       |+
!| ❗  18 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • local_component_structure - kraken2_standard_report.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - krona_cleanup.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - visualization_krona.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_complexityfiltering.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - profiling.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_hostremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_fastp.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_adapterremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - standardisation_profiles.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_adapterremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_filtering.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - nonpareil.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_hostremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-02-12 10:51:20

@sofstam sofstam marked this pull request as ready for review February 12, 2026 10:53
jfy133
jfy133 reviewed Feb 12, 2026
View reviewed changes
tests/minimal.nf.test
assertAll(
{ assert workflow.success},
{ assert snapshot(
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
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@jfy133 jfy133 Feb 12, 2026

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Missing sp[ecifiying stable_name_all here :)

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@jfy133 jfy133 jfy133 left review comments

@LilyAnderssonLee LilyAnderssonLee Awaiting requested review from LilyAnderssonLee LilyAnderssonLee is a code owner

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@sofstam @nf-core-bot @jfy133