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Merged
merged 5 commits into from
Aug 12, 2025
Merged

Publish selected .command files #235

merged 5 commits into from
Aug 12, 2025

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scwatts
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@scwatts scwatts commented Aug 12, 2025

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@scwatts scwatts requested a review from ohofmann August 12, 2025 01:18
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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: 3.3.1.
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 Aug 12, 2025 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit d70e494

+| ✅ 213 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗  13 tests had warnings |!
-| ❌   3 tests failed       |-

❌ Test failures:

  • files_unchanged - .gitignore does not match the template
  • schema_params - Default value for param processes_manual invalid: String should not be set to false
  • rocrate_readme_sync - The RO-Crate descriptions do not match the README.md content. Use nf-core lint --fix rocrate_readme_sync to update.

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_unchanged - LICENSE does not match the template
  • schema_params - Schema param panel not found from nextflow config
  • schema_params - Schema param fastp_umi_location not found from nextflow config
  • schema_params - Schema param fastp_umi_length not found from nextflow config
  • schema_params - Schema param fastp_umi_skip not found from nextflow config
  • schema_params - Schema param redux_umi_duplex_delim not found from nextflow config
  • schema_params - Schema param genome_version not found from nextflow config
  • schema_params - Schema param genome_type not found from nextflow config
  • schema_params - Schema param ref_data_hmf_data_path not found from nextflow config
  • schema_params - Schema param ref_data_panel_data_path not found from nextflow config
  • schema_params - Schema param ref_data_genome_gtf not found from nextflow config
  • schema_params - Schema param ref_data_hla_slice_bed not found from nextflow config

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.1
  • Run at 2025-08-12 02:12:49

ohofmann
ohofmann approved these changes Aug 12, 2025
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lgtm

@scwatts
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scwatts commented Aug 12, 2025

Forcing merge here to resolve CI/CD issues in the template PR

@scwatts scwatts merged commit f415035 into dev Aug 12, 2025
2 of 9 checks passed
@scwatts scwatts deleted the publish-selected-command-files branch August 12, 2025 02:12
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@ohofmann ohofmann ohofmann approved these changes

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@scwatts @nf-core-bot @ohofmann @luan-n-nguyen