Collapsing Second Pass v1.8.1

Version of tools in docker image (/container/Dockerfile)

Tool	Version	Location
java base image	8	-
Marianas	1.8.1	https://github.com/juberpatel/Marianas/releases/download/v1.8.1/Marianas-1.8.1.jar

CWL

• CWL specification 1.0

• Use example_inputs.yaml to see the inputs to the cwl

• Example Command using toil:

    > toil-cwl-runner marianas_first_pass.cwl test_inputs_second_pass.yaml