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fix(test): use small reference for MiniBWA - #225

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edmundmiller merged 1 commit into
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fix-minibwa-test-reference
Jul 16, 2026
Merged

fix(test): use small reference for MiniBWA#225
edmundmiller merged 1 commit into
devfrom
fix-minibwa-test-reference

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@edmundmiller

@edmundmiller edmundmiller commented Jul 16, 2026

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Summary

  • run the MiniBWA pipeline test against the chr21 nascent reference instead of full hg38
  • make the existing skip_pints.config actually skip PINTS_VISUALIZER

Verification

  • Nextflow 25.10.4, debug,test,docker: pipeline completed successfully with MiniBWA index construction and alignment
  • commit hooks passed

Fixes the resource failure observed after #221 without removing MiniBWA.

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github-actions Bot commented Jul 16, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3dba17c

+| ✅ 166 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗  23 tests had warnings |!
Details

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • readme - README did not have an nf-core template version badge.
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/nascent/nascent/subworkflows/local/prepare_genome.nf: _ versions = ch_versions.ifEmpty(null)
    _
  • local_component_structure - gtf2bed.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - bed2saf.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - quality_control.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_genome.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/nf-test.yml
  • files_exist - File is ignored: .github/actions/get-shards/action.yml
  • files_exist - File is ignored: .github/actions/nf-test/action.yml
  • files_exist - File is ignored: tests/default.nf.test
  • nextflow_config - nextflow_config
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/nf-core-nascent_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-nascent_logo_light.png
  • schema_params - schema_params

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-07-16 04:14:17

@edmundmiller
edmundmiller merged commit ebf514a into dev Jul 16, 2026
8 checks passed
@edmundmiller
edmundmiller deleted the fix-minibwa-test-reference branch July 16, 2026 19:20
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@edmundmiller