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Important! Template update for nf-core/tools v3.3.2 #40

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Merged
muffato merged 5 commits into from
Dec 2, 2025
Merged

Important! Template update for nf-core/tools v3.3.2 #40

muffato merged 5 commits into from
Dec 2, 2025

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@sanger-tolsoft
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@sanger-tolsoft sanger-tolsoft commented Dec 1, 2025

Version 3.3.2 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-3.3.2 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 v3.3.2 release page.

@sanger-tolsoft
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sanger-tolsoft commented Dec 1, 2025

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Dec 1, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f15e79a

+| ✅ 169 tests passed       |+
#| ❔  24 tests were ignored |#
!| ❗   8 tests had warnings |!
Details

❗ 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!
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_if_empty_null - ifEmpty(null) found in fasta_windows.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _
  • local_component_structure - extract_column.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - params_check.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - fasta_windows.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • files_exist - File is ignored: assets/multiqc_config.yml
  • files_exist - File is ignored: assets/nf-core-sequencecomposition_logo_light.png
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_exist - File is ignored: docs/images/nf-core-sequencecomposition_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-sequencecomposition_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • nextflow_config - Config default ignored: params.selected_fw_output
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-sequencecomposition_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-sequencecomposition_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-sequencecomposition_logo_dark.png
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sequencecomposition/sequencecomposition/.github/workflows/awstest.yml
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-12-01 20:26:42

DLBPointon
DLBPointon approved these changes Dec 2, 2025
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LGTM

@muffato muffato merged commit 8b67934 into dev Dec 2, 2025
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@muffato muffato deleted the nf-core-template-merge-3.3.2 branch December 2, 2025 10:04
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muffato commented Dec 2, 2025

Thanks both

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@prototaxites prototaxites prototaxites approved these changes

@DLBPointon DLBPointon DLBPointon approved these changes

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@sanger-tolsoft @muffato @prototaxites @DLBPointon