sample Cromwell usage with GCP Batch
jar file - we are using a self-compiled version of jar which has the Google Batch fix and GPU support which is not yet in the main branch. date: Nov 9, 2023
After installing java and download the jar file. These command can be executed:
Hello world example:
java -Dconfig.file=gcpbatch.conf -jar cromwell-87-cc50a1f-SNAP.jar run hello.wdl -i hello.inputs
deepVariant_WGS wdl example:
java -Dconfig.file=gcpbatchillumina.conf -jar cromwell-87-cc50a1f-SNAP.jar run deepVariant_WGS.wdl
GPU example - L4: l4 GPUs is associated with specific machine type: g2. Users do not need to specific the machine type in WDL file.
java -Dconfig.file=gcpbatch.conf -jar cromwell-87-cc50a1f-SNAP.jar run hello-gpu-l4.wdl
GPU example - A100: a100 GPUs is associated with specific machine type: a2. Users do not need to specific the machine type in WDL file.
java -Dconfig.file=gcpbatch.conf -jar cromwell-87-cc50a1f-SNAP.jar run hello-gpu-a100.wdl