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Important! Template update for nf-core/tools v3.4.1 #254

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Merged
scwatts merged 4 commits into from
Nov 11, 2025
Merged

Important! Template update for nf-core/tools v3.4.1 #254

scwatts merged 4 commits into from
Nov 11, 2025

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@nf-core-bot nf-core-bot commented Oct 16, 2025

Version 3.4.1 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-3.4.1 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 https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v3.4.1 release page.

@scwatts scwatts self-assigned this Nov 4, 2025
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github-actions bot commented Nov 5, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 431ed1c

+| ✅ 211 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗  17 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_unchanged - LICENSE does not match the template
  • 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
  • schema_description - No description provided in schema for parameter: prepare_reference_only

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.4.1
  • Run at 2025-11-10 23:44:56

@scwatts scwatts force-pushed the nf-core-template-merge-3.4.1 branch from 0a3c37b to 33f7c01 Compare November 5, 2025 05:08
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scwatts commented Nov 10, 2025

Force pushing again with a cleanly organised set of commits

@scwatts scwatts force-pushed the nf-core-template-merge-3.4.1 branch from dd900f7 to 431ed1c Compare November 10, 2025 23:43
@scwatts scwatts merged commit 823c9f9 into dev Nov 11, 2025
8 checks passed
@scwatts scwatts deleted the nf-core-template-merge-3.4.1 branch November 11, 2025 02:39
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