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Merged
scwatts merged 7 commits into from
Nov 30, 2025
Merged

Apply Hartwig updates, fixes #267

scwatts merged 7 commits into from
Nov 30, 2025

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@scwatts
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@scwatts scwatts commented Nov 28, 2025

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reecejones-hartwig and others added 7 commits September 29, 2025 15:43
@reecejones-hartwig
Update CIDER arguments and reference data
1c74264 
Switch from BLAST to BWA-MEM for query sequence search
@luan-n-nguyen
Update HMF containers and process labels
faf8980 
- BamTools to 1.5
- CIDER to 1.1
- COBALT to 2.2
- ESVEE to 1.2
- LILAC to 1.7.3
- LINX to 2.2
- ORANGE to 4.1.2
- PURPLE to 4.3
- REDUX to 1.2.2
- TEAL to 1.3.6
- VirusInterpreter to 1.7.2
@luan-n-nguyen
Remove realignment step in LILAC subworkflow
5533b93
@luan-n-nguyen
Update reference data
50ba994
@luan-n-nguyen
Update HMF tools arguments
126173e
@luan-n-nguyen
Update, reorganise usage documentation
099bc84 
- note requirements for REDUX input discovery on object stores
- promote compute resource to dedicated page
- update information on RNA panel reference data
@scwatts
Apply linting
c0c5aff
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github-actions bot commented Nov 28, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c0c5aff

+| ✅ 210 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 3.5.1
  • Run at 2025-11-28 02:51:03

@scwatts
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scwatts commented Nov 28, 2025

Test failures are to be addressed in #265

@scwatts scwatts merged commit 5f05a27 into dev Nov 30, 2025
6 of 8 checks passed
@scwatts scwatts deleted the hartwig-updates branch November 30, 2025 23:08
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@luan-n-nguyen luan-n-nguyen luan-n-nguyen approved these changes

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@scwatts @luan-n-nguyen @reecejones-hartwig