mobidic / Crom-wellWrapped

Wrapper for Cromwell execution

Crom-wellWrapped

Wrapper for Cromwell execution

Goals

Run Cromwell command with arguments checking, providing traceability with logs

Run

./cww.sh -e /PATH/TO/cromwell.jar -w workflow.wdl -i workflow_inputs.json 

Options

-c | --conf <file.conf> : To add a conf file
-o | --option <option.json> : To add an option file \ -v | --verbosity <1, 2, 3 or 4> : To set verbosity level (ERROR : 1 | WARNING : 2 | INFO [default] : 3 | DEBUG : 4)
-h | --help : Print help message in terminal and close the script \

Good to know

We recommend to name your input file as Broad did on WDL's tutorial : *_inputs.json