error polishing subworkflow based on DeepVariant - Githubissues

NBISweden / Earth-Biogenome-Project-pilot

Assembly and Annotation workflows for analysing data in the Earth Biogenome Project pilot project.

https://www.earthbiogenome.org/

GNU General Public License v3.0

9 stars 8 forks source link

error polishing subworkflow based on DeepVariant #100

Closed MartinPippel closed 2 weeks ago

MartinPippel commented 1 month ago

add dvpolish subworkflow
inputs: assembly, HiFi reads
output polished assembly
TODO's:
- compress output assembly
- run merqury pipeline to get QVs per contig, optional: select best contig version (polished vs unpolished)
- how to provide chunk_size as default parameter?
- create test suite
- add a coverage range (based on purge_dups thresholds?) and allow variant calls only within those ranges