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Update somatic vc subworkflow sage and manta#35

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subworkflow-vc-patch
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Update somatic vc subworkflow sage and manta#35
RaqManzano wants to merge 3 commits intodevfrom
subworkflow-vc-patch

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@RaqManzano RaqManzano commented Jul 23, 2024

Sage throws an error when resource files are not provided because and manta subworkflow needed to be updated.

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Update somatic vc subworkflow sage and manta
82360de 
Sage throws an error when resource files are not provided because and manta subworkflow needed to be updated.
@RaqManzano RaqManzano self-assigned this Jul 23, 2024
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github-actions bot commented Jul 23, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 923e897

+| ✅ 207 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  15 tests had warnings |!
Details

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: TODO nf-core:
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • 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 output.md: Write this documentation describing your workflow's output
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-23 07:37:30

@RaqManzano RaqManzano mentioned this pull request Jul 25, 2025
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