CWL docker containers can't mount paths with ':'

[mccalluc]

From Joel:

Interesting problem integrating Chuck's CWL workflow onto the salmon workflow: I can't call workflow.cwl in airflow because there are :'s in the paths for the directories in use. Airflow uses timestamps in the jobids, and the way things are set up now those id's get used in the path names. The extra :'s break the syntax of the docker volume specification, as below:

INFO [job workflow.cwl] /tmp/4cf898fg$ docker \
   run \
   -i \
   --volume=/tmp/4cf898fg:/HZfoyx:rw \
   --volume=/tmp/e8pu8i7i:/tmp:rw \
   --volume=/home/airflow/repositories/ingest-pipeline/src/ingest-pipeline/airflow/data/temp/trig_
_2020-02-08T22:34:44.290910+00:00/cwl_out/cluster-marker-genes:/var/lib/cwl/stg706d994b-d3e7-49fd-9
9a2-d236a8783326/cluster-marker-genes:ro \
   --workdir=/HZfoyx \
   --read-only=true \
   --user=1008:1008 \
...
docker: Error response from daemon: invalid volume specification: '/home/airflow/repositories/inges
t-pipeline/src/ingest-pipeline/airflow/data/temp/trig__2020-02-08T22:34:44.290910+00:00/cwl_out/clu
ster-marker-genes:/var/lib/cwl/stg706d994b-d3e7-49fd-99a2-d236a8783326/cluster-marker-genes:ro'.

[mccalluc]

I think --mount could be used instead. moby/moby#8604 (comment) (and further down that thread, if the commas become an issue, the args can be quoted like a CSV.)