Common Workflow Language

CWL documents describe workflows made of command line data analysis tools in a portable, reproducible, and reusable fashion.

As requested in https://gitter.im/bd2k-genomics-toil/Lobby?at=617126297db1e3753e527ff2 it would be useful for debugging to be able to stop the whole workflow as soon as a single job fails, even if other jobs still exist to be run or are currently running.

┆Issue is synchronized with this Jira Task
┆Issue Number: TOIL-1062

Expected Behavior

cwltool ignores default values when using the argument on the command line

Actual Behavior

Calling cwltool with an argument that is a string[] in the command line will keep the the default value in the array.
Does not happen when using a yaml file as input.

Workflow Code

#!/usr/bin/env cwl-runner

cwlVersion: v1.2
class: CommandLineTool

baseCommand:

Common Workflow Language

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