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Migrate to the 3.5.1 template with nf-migrate - #133

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Skitionek merged 1 commit into
nf-core-template-merge-3.5.1from
nf-migrate-3.5.1-migration
Oct 27, 2026
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Migrate to the 3.5.1 template with nf-migrate#133
Skitionek merged 1 commit into
nf-core-template-merge-3.5.1from
nf-migrate-3.5.1-migration

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@Skitionek

@Skitionek Skitionek commented Oct 16, 2026

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Migrates the pipeline to the 3.5.1 nf-core template with nf-migrate, keeping the pipeline's own files where it diverged.

relates to #123

Coding and writing assisted with Sonnet 5.5

@Skitionek
feat: migrate to the nf-core template with nf-migrate
f863b65 
Result of nf-migrate merge-template for the 3.5.1 template; the pipeline's own files are kept where it has diverged from the template.

Coding/Writing assisted with Sonnet 5.5

Prompts:
- Resolve #123 with nf-migrate and open two stacked draft PRs.
@github-actions

github-actions Bot commented Oct 16, 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: 3.5.1.
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 Oct 16, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f863b65

+| ✅ 213 tests passed       |+
#| ❔   4 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   8 tests had warnings |!
Details

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 main.nf.test: Once you have added the required tests, please run the following command to build this file:
  • 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
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • 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)

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File does not exist: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-10-16 14:13:09

@github-actions

github-actions Bot commented Oct 16, 2026

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❌ nf-test failed with latest Nextflow version

Note

Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing.

  • ❌ docker | latest-everything | Shard 1/1

See the full run for details.

@Skitionek
Skitionek marked this pull request as ready for review October 16, 2026 14:17
@Skitionek Skitionek self-assigned this Oct 20, 2026
Base automatically changed from nf-migrate-3.5.1-merge-dev to nf-core-template-merge-3.5.1 October 27, 2026 19:54
@Skitionek
Skitionek merged commit d86fcf2 into nf-core-template-merge-3.5.1 Oct 27, 2026
8 checks passed
@Skitionek
Skitionek deleted the nf-migrate-3.5.1-migration branch October 27, 2026 19:54
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