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Merged
muffato merged 1 commit into from
Dec 2, 2025
Merged

Update all modules #41

muffato merged 1 commit into from
Dec 2, 2025

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@muffato
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@muffato muffato commented Dec 2, 2025

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
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile 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).

@muffato muffato self-assigned this Dec 2, 2025
@sanger-tolsoft
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sanger-tolsoft commented Dec 2, 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 2, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit be46825

+| ✅ 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 2025-12-02 10:31:04

@muffato muffato merged commit 8779718 into dev Dec 2, 2025
7 checks passed
@muffato muffato deleted the modules_update branch December 2, 2025 10:35
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@muffato @sanger-tolsoft