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Implement nf-test#475

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edmundmiller merged 4 commits intodevfrom
nftest-implementation
Sep 5, 2025
Merged

Implement nf-test#475
edmundmiller merged 4 commits intodevfrom
nftest-implementation

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@edmundmiller edmundmiller commented Sep 3, 2025 •
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Moves the basic CI test over test after the template update #473

@edmundmiller edmundmiller added this to the 2.2 milestone Sep 3, 2025
@edmundmiller edmundmiller self-assigned this Sep 3, 2025
@edmundmiller edmundmiller marked this pull request as draft September 3, 2025 17:57
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github-actions Bot commented Sep 3, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 779ce9a

+| ✅ 269 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  34 tests had warnings |!
Details

❗ Test warnings:

  • 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 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 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_if_empty_null - ifEmpty(null) found in prepare_genome.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _
  • local_component_structure - igv.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - star_align.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - gtf2bed.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - macs3_consensus.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - bam_remove_orphans.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - plot_homer_annotatepeaks.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - bedtools_genomecov.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - genome_blacklist_regions.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - multiqc.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - plot_macs3_qc.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - samplesheet_check.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - multiqc_custom_phantompeakqualtools.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - bamtools_filter.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - multiqc_custom_peaks.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - deseq2_qc.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - star_genomegenerate.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - annotate_boolean_peaks.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - frip_score.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - bam_peaks_call_qc_annotate_macs3_homer.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - bam_filter_bamtools.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
  • local_component_structure - bam_bedgraph_bigwig_bedtools_ucsc.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - align_star.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - input_check.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.bamtools_filter_pe_config
  • nextflow_config - Config default ignored: params.bamtools_filter_se_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-09-05 04:00:48

@edmundmiller edmundmiller force-pushed the nftest-implementation branch 4 times, most recently from 4ad48c4 to 0ff351d Compare September 4, 2025 14:00
@edmundmiller edmundmiller force-pushed the nftest-implementation branch 2 times, most recently from 279a9f3 to 8f4f416 Compare September 4, 2025 20:11
edmundmiller and others added 2 commits September 4, 2025 22:58
@edmundmiller @claude
test: Implement nft-utils for enhanced snapshot testing
4655769 
- Update nft-utils plugin from v0.0.3 to v0.0.5
- Replace basic snapshot assertions with nft-utils functions:
  - Use removeNextflowVersion() to eliminate timestamp variations
  - Add getAllFilesFromDir() for comprehensive file structure snapshots
  - Exclude unstable execution files for consistent CI testing
- Enhance all test files: bowtie2, chromap, star, skip_trimming, skip_consensus_peaks
- Maintain correct test expectations (main tests fail, stub tests pass)

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>
@edmundmiller
style: The RO-Crate descriptions do not match the README.md content
779ce9a
@edmundmiller edmundmiller marked this pull request as ready for review September 5, 2025 12:59
maxulysse
maxulysse reviewed Sep 5, 2025
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Comment thread .gitignore
testing*
*.pyc
null/

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Suggested change

maxulysse
maxulysse reviewed Sep 5, 2025
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Comment thread modules/local/multiqc.nf
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todo
out of scope.
But why is MultiQC a local module?

maxulysse
maxulysse reviewed Sep 5, 2025
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Comment thread tests/nextflow.config
Comment on lines +7 to +15
// Limit resources so that this can run on GitHub Actions
process {
resourceLimits = [
cpus: 2,
memory: '6.GB',
time: '6.h'
]
}

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question
we shouldn't need this if we run all with profile test, no?

@github-project-automation github-project-automation Bot moved this from Todo to In Progress in nf-test Migration Sep 5, 2025
@edmundmiller edmundmiller merged commit cd1f242 into dev Sep 5, 2025
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@github-project-automation github-project-automation Bot moved this from In Progress to Done in nf-test Migration Sep 5, 2025
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@maxulysse maxulysse maxulysse approved these changes

@pinin4fjords pinin4fjords pinin4fjords approved these changes

@JoseEspinosa JoseEspinosa Awaiting requested review from JoseEspinosa

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nf-test Migration
Status: Done

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@edmundmiller @maxulysse @pinin4fjords
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