Site-specific hooks

Built specifically for Clinical Genomics Lund’s BJORN system.

reformat-csv

Reformat a BJORN microbiology CSV (and optionally SH) file for JASEN.

jasentool reformat-csv --csv-file <FILE> --output-file <FILE>
                        [--sh-file <FILE>] [--remote-dir <DIR>] [--remote-hostname <HOST>]
                        [--remote] [--auto-start] [--alter-sample-id]

Argument	Required	Default	Description
--csv-file	Yes	—	Path to BJORN CSV file
-o/--output-file	Yes	—	Path to fixed output CSV file
--sh-file	No	None	Path to BJORN SH file
--remote-dir	No	/fs1/bjorn/jasen	Remote directory for spring files
--remote-hostname	No	rs-fe1.lunarc.lu.se	Remote hostname
--remote	No	False	Enable remote copy
--auto-start	No	False	Automatically start after fix
--alter-sample-id	No	False	Alter sample ID to LIMS ID + sequencing run

Example

jasentool reformat-csv \
  --csv-file bjorn.csv \
  --output-file fixed.csv \
  --sh-file bjorn.sh \
  --remote