mobidic / MobiDL-dev

Developement of new pipeline from MobiDL

MobiDL

MobidicWDL-dev workflow

Goals

Providing wdl workflows to treat NGS data (dev)

Repos architecture and requirements

• Each step can be found in dedicated wdls in modules/

• A workflow imports individual wdls and run them, see panelCapture.wdl for details

• json files are provided as examples, work at mobidic institution on minimonster

• needs crowmwell to run

validate a workflow

• requires womtools

java -jar /PATH/TO/womtool.jar validate panelCapture.wdl 

run

java -jar /PATH/TO/cromwell.jar run panelCapture.wdl -i panelCapture_inputs.json