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.

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

Update nextflow_wgs to DSL2 #274

Merged
merged 325 commits into from
Jan 31, 2025
Merged

Update nextflow_wgs to DSL2 #274

merged 325 commits into from
Jan 31, 2025

Conversation

alkc
Copy link
Contributor

@alkc alkc commented Dec 16, 2024

Description and reviewer info

Closes #255, fixes #291

The purpose of this PR is to migrate nf_wgs over to DSL2. This does not entail corralling the processes into workflows.
A few processes have been removed, such as the melt_qc_val. Annotation only runs will need to be re-added in some future PR.

Type of change

  • Documentation
  • Patch
  • Minor change
  • Major change

Checklist

  • Self-review of my code
  • Update the CHANGELOG
  • Tag the latest commit (vX.Y.Z format)

Major / Minor change

  • Stub run completes without errors or new warnings
  • GIAB single (wgs) finishes and differences to current master branch have been investigated (using PipeEval)
  • GIAB trio (wgs) finishes and differences to current master branch have been investigated
  • Seracare (onco) sample finishes and differences to current master branch have been investigated
  • Output from processes with altered code have been inspected (i.e. in the work folder: .command.sh, .command.log, .command.err and result files)
  • All three samples can be loaded into Scout
  • test mody sample
  • test myeloid-const (does the no-sv loqus workaround still work?)
  • At least one other person has reviewed and approved my code
  • I have made corresponding changes to the documentation (software versions, etc.)

Test/review documentation

Review performed by

  • Alexander
  • Jakob
  • Paul
  • Ryan
  • Viktor

Testing performed by

  • Alexander
  • Jakob
  • Paul
  • Ryan
  • Viktor

@alkc alkc self-assigned this Dec 16, 2024
@alkc alkc marked this pull request as draft December 16, 2024 10:56
@alkc alkc added status: draft epic Theme of work that contains subtasks labels Dec 16, 2024
@alkc
Copy link
Contributor Author

alkc commented Dec 18, 2024

at this point the enabled processes pass stub runs for giab-trio and seracare

@alkc
Copy link
Contributor Author

alkc commented Jan 30, 2025

scout sample load checklist:

  • seracare
  • giab trio
  • giab single

@alkc alkc merged commit 7f9cc03 into master Jan 31, 2025
2 checks passed
@alkc alkc deleted the alkc/dsl2 branch January 31, 2025 12:08
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
epic Theme of work that contains subtasks status: draft
Projects
None yet
Development

Successfully merging this pull request may close these issues.

Output Gens data when starting from bam Rewrite pipeline into DSL2
2 participants