This container and cwl wrapper define a way to run OpenCRAVAT within CWL on platforms such as DNANexus and SevenBridges. Modules are tarred and gzipped and passed as inputs to the cwl job. They are unzipped within the container before OpenCRAVAT runs.
Build the container at container/Dockerfile
OC-CWL module archives are a .tgz archive of an oc modules directory containing one or more modules. Before the job runs, the module archives are unzipped to create a combined mdir.
Some example module archives are temporarily available here
From the above link, place base.tgz, clinvar.tgz, and go.tgz into the modules directory, then run
cwl-runner oc.cwl job.cwl
From the above link, place base.tgz, clinvar.tgz, and go.tgz into the modules directory, then run
cwl-runner oc-workflow.cwl job.cwl
The container can be run without cwl as follows.
docker run -v $PWD:/tmp/job -v $PWD/modules:/tmp/modules oc oc --modules /tmp/modules/base.tgz /tmp/modules/clinvar.tgz /tmp/modules/go.tgz run /tmp/job/input.txt -l hg38