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Merged
merged 4 commits into from
Apr 25, 2025
Merged

Add ruff to pre-commit checks #464

merged 4 commits into from
Apr 25, 2025

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grst
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@grst grst commented Apr 24, 2025 •
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Add Ruff as linter/autoformatter

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/scrnaseq 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 Apr 24, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit cda15ea

+| ✅ 215 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  20 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!
  • schema_description - No description provided in schema for parameter: skip_emptydrops
  • local_component_structure - gtf_gene_filter.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - parse_cellrangermulti_samplesheet.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - alevinqc.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - anndatar_convert.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - mtx_to_h5ad.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - gffread_transcriptome.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 - concat_h5ad.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - align_cellrangerarc.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - fastqc.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - simpleaf.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - kallisto_bustools.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - align_cellrangermulti.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - h5ad_conversion.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - starsolo.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - align_cellranger.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-04-24 06:44:24

@grst grst requested review from nictru and mashehu April 24, 2025 06:44
nictru
nictru approved these changes Apr 24, 2025
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LGTM

Just one note, some time ago I created this shared module for filtering the GTF based on FASTA. Maybe it is useful for scrnaseq

@grst grst mentioned this pull request Apr 24, 2025
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grst commented Apr 24, 2025

Apparently unrelated failure on latest-everything:

Receiver class nextflow.validation.ValidationObserver does not define or inherit an implementation of the resolved method 'abstract void onFilePublish(java.nio.file.Path, java.nio.file.Path, java.util.Map)' of interface nextflow.trace.TraceObserver.

--> failure to publish files

@grst grst mentioned this pull request Apr 24, 2025
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nictru commented Apr 24, 2025

This errors can be ignored for now, based on this message

@grst grst merged commit 996b0ae into dev Apr 25, 2025
11 of 18 checks passed
@grst grst deleted the pre-commit-python branch April 25, 2025 07:00
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@mashehu mashehu mashehu approved these changes

@nictru nictru nictru approved these changes

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