A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Make total sense. I forked both repos and opened PRs.

Added some comments in the PR. Some are major and important to get fixed.

PS: would appreciate if you did some testing of your branch using some real samples you have. So you know it actually works :stuck_out_tongue:

Tested on my own data (subset for chr5+chr19 for speed), full SAVANA_RUN → CLASSIFY → CNA chain completes end-to-end with a real purity/ploidy fit and a proper segmented copy-number profile backed by thousands of het-SNPs per segment.

Thanks I'll have a look. Did you close the main PR by accident or is it still in progress?