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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Updated JASEN to support PRP v0.10.0 #338

Closed mhkc closed 2 months ago

mhkc commented 3 months ago

Description

##Remove elements in cursive as needed.##

If not self-evident, mention what prompted the change.

Summary of the changes made:

Primary function of PR

[ ] Hotfix
[x] Minor functionality improvement
[ ] Major functionality improvement / New type of analysis
[ ] Backward-breaking functionality

Testing

Either describe a procedure, or add data; that confirms that the PR resolves what it sets out to do

Sign-offs

[ ] Code reviewed by @octocat
[ ] Code tested by @octocat

ryanjameskennedy commented 3 months ago

Should we run this for adding the bam and symlinkDir? We already add these using prp create-bonsai-input. I think we should either move these to prp add-igv-annotation-track or vice versa. I also think this is not very explicit despite these files being explicitly for a purpose.