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updating gens subworkflow #515

Merged
merged 9 commits into from
Feb 14, 2024
Merged

updating gens subworkflow #515

merged 9 commits into from
Feb 14, 2024

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jemten
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@jemten jemten commented Feb 13, 2024 •
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PR checklist

This PR updates the gens pre-processing subworkflow to.
Changes include:

  • New docker image
  • Fail with error message when trying to run gens with conda
  • Male and female samples now uses different panel of normals, given using the params --gens_pon_female and --gens_pon_male
  • Use gvcf rather than vcf
  • renamed the gens controller option from --gens_switch to --skip_gens (true by default)

``

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/raredisease branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Feb 13, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 48cf0b3

+| ✅ 182 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowRaredisease.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-14 12:38:06

@jemten jemten marked this pull request as ready for review February 13, 2024 16:48
ramprasadn
ramprasadn approved these changes Feb 14, 2024
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LGTM 👍🏻

@jemten jemten merged commit 27f0aae into nf-core:dev Feb 14, 2024
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@ramprasadn ramprasadn ramprasadn approved these changes

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@jemten @ramprasadn