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Update PAVE somatic command #87

Merged
merged 1 commit into from
Aug 15, 2024
Merged

Update PAVE somatic command #87

merged 1 commit into from
Aug 15, 2024

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scwatts
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@scwatts scwatts commented Aug 15, 2024

  • previously the PAVE command followed the Pv5 implementation
  • the recommendation is now to run PAVE always with the -clinvar_vcf argument
  • similarly, the -blacklist_bed and -blacklist_vcf should now only be used for PAVE germline
  • both changes are also recommended irrespective of sequence type (wgts/targeted) or analysis type (tn/to)

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github-actions bot commented Aug 15, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 41b962e

+| ✅ 177 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗  13 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • nextflow_config - Config manifest.version should end in dev: 1.0.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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!
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • schema_params - Schema param panel 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_virusbreakenddb_path 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 2.14.1
  • Run at 2024-08-15 05:05:24

@scwatts scwatts marked this pull request as ready for review August 15, 2024 05:06
@scwatts scwatts merged commit 42ee926 into dev Aug 15, 2024
4 checks passed
@scwatts scwatts deleted the update-pave-somatic-command branch August 15, 2024 22:24
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@charlesshale charlesshale charlesshale approved these changes

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@scwatts @charlesshale