The stager.py script copies all inputs to a cwl workflow into a single location
in order to cut down on unnecessary file copying as Cromwell runs. To use, run
python /usr/bin/stager.py <input yaml | input json> <staging_directory> <workflow.cwl>
within the mgibio/standalone-input-staging docker image.
It outputs a new yaml file, with "staged_" prepended to the name of the input
yaml; this new file can then be used as normal to run the workflow. 

Currently, files with the same name will be ignored. This will likely change
once we have discussed how we want to handle this. The workflow.cwl file must
be passed to the script to properly capture secondaryFiles; upcoming updates
will make parsing this file safer, but won't change the usage or output of the
script. Currently, this can only be used as a standalone script, but there is
a workaround that may allow this to be run as part of a workflow, if needed. It
may also allow for links to be passed to Cromwell and then used normally,
without the need for copying.