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Switch GRCh38_hmf to the new ALT masked genome #161

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Merged
merged 1 commit into from
Mar 11, 2025
Merged

Switch GRCh38_hmf to the new ALT masked genome #161

merged 1 commit into from
Mar 11, 2025

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scwatts
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@scwatts scwatts commented Mar 10, 2025

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@scwatts scwatts requested a review from qclayssen March 10, 2025 23:58
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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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github-actions bot commented Mar 11, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 33b6eb8

+| ✅ 198 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗  18 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 nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • 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 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_virusbreakenddb_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 2025-03-11 00:00:02

@scwatts scwatts merged commit 06bc3a0 into dev Mar 11, 2025
6 checks passed
@scwatts scwatts deleted the use-grch38-hmf-alt-masked branch March 11, 2025 01:00
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scwatts commented Apr 5, 2025

Superseded by:

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@qclayssen qclayssen qclayssen approved these changes

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@scwatts @nf-core-bot @qclayssen
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