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Important! Template update for nf-core/tools v3.4.1 #496

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Merged
Parent: Release version 4.1.0 of pipeline
merged 4 commits into from
Oct 24, 2025
Merged

Important! Template update for nf-core/tools v3.4.1 #496

merged 4 commits into from
Oct 24, 2025

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Version 3.4.1 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-3.4.1 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v3.4.1 release page.

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github-actions bot commented Oct 22, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b85978b

+| ✅ 241 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗  21 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 4.1.0
  • 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!
  • schema_description - No description provided in schema for parameter: skip_emptydrops
  • local_component_structure - mtx_to_h5ad.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 - parse_cellrangermulti_samplesheet.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 - concat_h5ad.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 - gtf_gene_filter.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - fastqc.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_cellrangerarc.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 - h5ad_conversion.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 - kallisto_bustools.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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.4.1
  • Run at 2025-10-23 18:05:38

@nictru nictru requested review from fmalmeida and grst October 23, 2025 18:22
@grst grst merged commit 5b28513 into dev Oct 24, 2025
20 checks passed
@grst grst deleted the nf-core-template-merge-3.4.1 branch October 24, 2025 06:01
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@grst grst grst approved these changes

@fmalmeida fmalmeida Awaiting requested review from fmalmeida

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@nf-core-bot @grst @nictru