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Important! Template update for nf-core/tools v3.5.1 #140

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Merged
muffato merged 6 commits into from
Dec 8, 2025
Merged

Important! Template update for nf-core/tools v3.5.1 #140

muffato merged 6 commits into from
Dec 8, 2025

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@sanger-tolsoft
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@sanger-tolsoft sanger-tolsoft commented Dec 2, 2025

Version 3.5.1 of nf-core/tools has just been released with updates to the nf-core template. For more details, check out the blog post: None

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-3.5.1 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 v3.5.1 release page.

Note

Since nf-core/tools 3.5.0, older template update PRs will not be automatically closed, but will remain open in your pipeline repository. Older template PRs will be automatically closed once a newer template PR has been merged.

@gq1 gq1 mentioned this pull request Dec 2, 2025
Merged
@gq1 gq1 closed this Dec 3, 2025
@gq1 gq1 deleted the nf-core-template-merge-3.5.1 branch December 3, 2025 10:25
@muffato muffato restored the nf-core-template-merge-3.5.1 branch December 5, 2025 17:19
@muffato muffato reopened this Dec 5, 2025
@muffato muffato self-assigned this Dec 5, 2025
@muffato muffato linked an issue Dec 5, 2025 that may be closed by this pull request
Update pipeline template #106
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github-actions bot commented Dec 5, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4b8ca2d

+| ✅ 167 tests passed       |+
#| ❔  26 tests were ignored |#
!| ❗  14 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes_ignored.config
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • 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
  • local_component_structure - pacbio_filter.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - input_merge.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - process_vcf.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - input_filter_split.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - filter_pacbio.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - deepvariant_caller.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - align_pacbio.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - convert_stats.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-variantcalling_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-variantcalling_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-variantcalling_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
  • files_exist - File is ignored: assets/multiqc_config.yml
  • files_exist - File is ignored: conf/igenomes.config
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • nextflow_config - Config default ignored: params.vector_db
  • 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/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-variantcalling_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-variantcalling_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-variantcalling_logo_dark.png
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/variantcalling/variantcalling/.github/workflows/awstest.yml
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2025-12-08 11:57:09

@muffato
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muffato commented Dec 5, 2025

test_align now fixed and implemented in nf-test. CRAM files have to be excluded because they're generated with a recent samtools in CRAM v3.1 (current default), which htsjdk doesn't support yet.

prototaxites
prototaxites approved these changes Dec 8, 2025
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LGTM!

prototaxites
prototaxites reviewed Dec 8, 2025
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@muffato muffato merged commit 7832ba4 into dev Dec 8, 2025
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@muffato muffato deleted the nf-core-template-merge-3.5.1 branch December 8, 2025 12:16
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Update pipeline template

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