Skip to content

Feature/prs utils - #3

Merged
Jorisvansteenbrugge merged 3 commits into
mainfrom
feature/prs_utils
Aug 5, 2026
Merged

Feature/prs utils#3
Jorisvansteenbrugge merged 3 commits into
mainfrom
feature/prs_utils

Conversation

@Jorisvansteenbrugge

Copy link
Copy Markdown
Collaborator

the scripts in here were already reviewed as part of DxNextflowPRS, they are moved here to organize the related stand-alone scripts into a bundled package

@github-actions

github-actions Bot commented Aug 5, 2026

Copy link
Copy Markdown

Coverage

Coverage Report
FileStmtsMissCoverMissing
src/prs_utils
   __init__.py00100% 
   cli.py27485%50, 59, 77, 88
   get_snp_list.py30293%19, 50
   merge_prs_mqc.py42198%75
   normalise_counts.py19195%33
   pgs_to_vcf.py95397%52–53, 134
   sample_qc.py42198%157
TOTAL2551295% 

Tests Skipped Failures Errors Time
23 0 💤 0 ❌ 0 🔥 2.893s ⏱️

@rernst
rernst self-requested a review August 5, 2026 12:22

@rernst rernst left a comment

Copy link
Copy Markdown
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

For now as a v1 and first replacement of the code in the modules repo this is fine. In a future version it would be nice to create a common cli using typer with subcommands for each utility function.

@Jorisvansteenbrugge
Jorisvansteenbrugge merged commit 9fabd8f into main Aug 5, 2026
2 checks passed
@Jorisvansteenbrugge
Jorisvansteenbrugge deleted the feature/prs_utils branch August 5, 2026 14:37
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants