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Important! Template update for nf-core/tools v4.0.3 - #66

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Important! Template update for nf-core/tools v4.0.3#66
nf-core-bot wants to merge 3 commits into
devfrom
nf-core-template-merge-4.0.3

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@nf-core-bot

@nf-core-bot nf-core-bot commented Jul 24, 2026

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Version 4.0.3 of nf-core/tools has just been released with updates to the nf-core template. For more details, check out the blog post: https://nf-co.re/advisories/pr-comment-workflow-vulnerability

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-4.0.3 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 the template sync documentation.

For more information about this release of nf-core/tools, please see the v4.0.3 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.

nf-core-bot and others added 2 commits July 24, 2026 12:35
@nf-core-bot
Template update for nf-core/tools version 4.0.3
77738d5
@apeltzer
Merge dev into nf-core-template-merge-4.0.3
e1d29fa 
- Remove fastqc module (not used in datasync pipeline)
- Add rclone/check, rclone/checksum, rclone/copy modules
- Update multiqc to v1.35 with updated containers
- Update nf-schema plugin to 2.7.2
- Use datasync-specific test-datasets base path
- Update container configs (remove fastqc, add rclone)
- Use actual datasync workflow implementation from dev
- Update nextflow_schema.json (copy_matching_only replaces igenomes_base)
- Update schema_input.json for datasync samplesheet format
- Keep nf-core template 4.0.3 version and updated GitHub action hashes
@github-actions

github-actions Bot commented Jul 30, 2026

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.3.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

@github-actions

github-actions Bot commented Jul 30, 2026 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 371ae90

+| ✅ 204 tests passed       |+
#| ❔   4 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  22 tests had warnings |!
-| ❌   1 tests failed       |-
Details

❌ Test failures:

  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • 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 nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • 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 CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.3
  • Run at 2026-07-30 09:55:34

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@nf-core-bot @apeltzer