Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Remove Strelka tumor-only somatic variant calling #1709

Merged
merged 5 commits into from
Oct 29, 2024
Merged

Remove Strelka tumor-only somatic variant calling #1709

merged 5 commits into from
Oct 29, 2024

Conversation

nevinwu
Copy link

@nevinwu nevinwu commented Oct 29, 2024 •
edited
Loading

Closes #803.

I have removed strelka tumor-only somatic variant calling from the bam_variant_calling_tumor_only_all subworkflow. Also i have updated the subway image, docs and tests.

Maybe we should leave the PR open for a few days to see if anyone complains about removing it: https://nfcore.slack.com/archives/CGFUX04HZ/p1730110553053079

PR checklist

  • 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/sarek 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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,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).

@github-actions GitHub Actions
Copy link

github-actions bot commented Oct 29, 2024 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e474240

+| ✅ 215 tests passed       |+
#| ❔  11 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • 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 base.config: Check the defaults for all processes

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-29 10:28:47

@maxulysse
Copy link
Member

issue with controlfreec test

@maxulysse
Copy link
Member

Seems to be a random issue, so I'll retrigger

@maxulysse maxulysse merged commit 1ba8cee into nf-core:dev Oct 29, 2024
53 of 57 checks passed
@nevinwu nevinwu deleted the dev branch October 29, 2024 11:48
@FriederikeHanssen
Copy link
Contributor

@rannick tagging you so we don't forget. We can easily revert this PR, if this feature is critical to you :)

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen is a code owner

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@nevinwu @maxulysse @FriederikeHanssen