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Dev fix ci simpleaf #442

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Merged
merged 7 commits into from
Mar 5, 2025
Merged

Dev fix ci simpleaf #442

merged 7 commits into from
Mar 5, 2025

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@apeltzer
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@apeltzer apeltzer commented Mar 5, 2025 •
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Hi @DongzeHE - this only addressed the lint fail from the multiqc config yaml.

@apeltzer apeltzer requested a review from DongzeHE March 5, 2025 20:14
@apeltzer apeltzer enabled auto-merge March 5, 2025 20:15
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github-actions bot commented Mar 5, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit db0c1dc

+| ✅ 214 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  21 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.1.0
  • 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 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!
  • local_component_structure - alevinqc.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 - parse_cellrangermulti_samplesheet.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - gtf_gene_filter.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 - anndatar_convert.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 - h5ad_conversion.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
  • local_component_structure - align_cellrangermulti.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 - 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_cellrangerarc.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 2025-03-05 20:16:06

@apeltzer apeltzer merged commit 065c73f into dev Mar 5, 2025
14 checks passed
@apeltzer apeltzer deleted the dev-fix-ci-simpleaf branch March 5, 2025 20:41
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@mashehu mashehu mashehu approved these changes

@DongzeHE DongzeHE Awaiting requested review from DongzeHE

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@apeltzer @mashehu @an-altosian @DongzeHE