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Merged
Parent: Release version 4.1.0 of pipeline
merged 7 commits into from
Aug 4, 2025
Merged

Bump version 4.1.0 for release #484

merged 7 commits into from
Aug 4, 2025

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@fmalmeida
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Hi @grst ,
Performed the bump-version steps in the "Steps for release" section described here:
https://nf-co.re/docs/checklists/pipeline_release#steps-to-release

Once merged, we can perform the release steps dev -> master.

@fmalmeida fmalmeida requested a review from grst August 1, 2025 13:01
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github-actions bot commented Aug 1, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 22a4cb3

+| ✅ 245 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 - 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 - alevinqc.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 - concat_h5ad.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 - parse_cellrangermulti_samplesheet.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_cellrangerarc.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 - starsolo.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 - fastqc.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 - 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 3.3.2
  • Run at 2025-08-04 10:24:18

@fmalmeida fmalmeida mentioned this pull request Aug 1, 2025
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grst commented Aug 4, 2025 •
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The CHANGELOG was missing some entries... I added them.

Seems like the version is encoded in the nf-test snapshots causing the tests to fail. The version should probably not be there at all? @fmalmeida can you please address this?

@fmalmeida
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Hi @grst ,
Added the changes required here: #487

@grst grst merged commit eaabd38 into dev Aug 4, 2025
20 checks passed
@grst grst deleted the bump-version-4.1.0 branch August 4, 2025 10:45
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@fmalmeida @grst