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Fix ctatsplicing ref building trigger #716

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Fix ctatsplicing ref building trigger #716

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@rannick rannick commented Jul 17, 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
  • If necessary, also make a PR on the nf-core/rnafusion branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

@rannick rannick self-assigned this Jul 17, 2025
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nf-core-bot commented Jul 17, 2025

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.2.1.
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 Jul 17, 2025 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit e67bd20

+| ✅ 293 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   8 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

  • schema_params - Default value for param ctatsplicing_ref invalid: Not in pipeline parameters. Check nextflow.config.

❗ 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: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • pipeline_if_empty_null - ifEmpty(null) found in main.nf: _ stringtie_gtf = ch_stringtie_gtf.ifEmpty(null) // channel: [meta, gtf]
    _
  • schema_lint - Input mimetype is missing or empty
  • schema_params - Schema param ctatsplicing_ref not found from nextflow config
  • local_component_structure - fusioninspector_workflow.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • files_exist - File is ignored: tests/default.nf.test
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-08-25 14:40:46

@atrigila atrigila linked an issue Aug 20, 2025 that may be closed by this pull request
ctatsplicing reference building triggering #704
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@nvnieuwk nvnieuwk Awaiting requested review from nvnieuwk nvnieuwk will be requested when the pull request is marked ready for review nvnieuwk is a code owner

@atrigila atrigila Awaiting requested review from atrigila atrigila will be requested when the pull request is marked ready for review atrigila is a code owner

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ctatsplicing reference building triggering

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