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Fix REDUX TSV discovery for non-local files #201

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Merged
merged 2 commits into from
May 12, 2025
Merged

Fix REDUX TSV discovery for non-local files #201

merged 2 commits into from
May 12, 2025

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scwatts
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@scwatts scwatts commented May 12, 2025

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@scwatts scwatts requested a review from qclayssen May 12, 2025 03:01
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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: 3.0.2.
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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scwatts commented May 12, 2025

Force pushing with commits rebased on top of dev

@scwatts scwatts force-pushed the fix-redux-tsv-discovery branch from 17324e2 to 2b88f15 Compare May 12, 2025 03:05
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github-actions bot commented May 12, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2b88f15

+| ✅ 197 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗  16 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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!
  • 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 3.0.2
  • Run at 2025-05-12 03:06:38

@scwatts scwatts merged commit 067e21a into dev May 12, 2025
6 checks passed
@scwatts scwatts deleted the fix-redux-tsv-discovery branch May 12, 2025 03:23
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@qclayssen qclayssen qclayssen approved these changes

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@scwatts @nf-core-bot @qclayssen
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