/MobiDL-dev

Developement of new pipeline from MobiDL

Primary LanguageWDLGNU General Public License v3.0GPL-3.0

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

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

run

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