genomic-medicine-sweden / jasen

Bacterial typing pipeline for clinical NGS data. Written in NextFlow, Python & Bash.

https://jasen.readthedocs.io/en/latest/

GNU General Public License v3.0

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Update to v0.9.0 #342

Closed ryanjameskennedy closed 2 months ago

ryanjameskennedy commented 2 months ago

Description

Summary of the changes made:

Added long-read test data (S. aureus)
Added samplelist_nanopore.csv for running long-read test data
Added location of documentation to README
Added cdmDir to config
Added process for adding IGV annotation tracks with PRP.
Updated how mycobacterium_tuberculosis workflow adds IGV annotation tracks.
Fixed --qc argument filepath to be full filepath to output
Fixed tbprofiler url in container Makefile
Fixed TB installation steps in main Makefile
Updated TbProfiler to version 6.3
Updated PRP to version 0.10.0
Removed delly annotation
Updated vcf args in prp module

Primary function of PR

[x] Major functionality improvement / New type of analysis

Testing

Tested on ecoli, saureus and tb samples