For WDL questions, see the WDL specification and WDL docs.
For Cromwell questions, see the Cromwell docs and please post any issues on Github.
How to develop WDL workflows using Docker images locally which can be used seamlessly in the cloud
Hi Broad/WDL folks,
I love WDL and we're really excited it's potential (good work!)
One question that I have about it is about what the workflow looks like for developing WDL programs locally (on a Mac) and then deploying those on the cloud (Google). How do you do this at Broad?
From here (https://docs.google.com/document/d/1jv4FFWC0RJUWoQagh7wA7L7K6lHNz72zGttwEfVKgnA/edit?ts=5601ad23#heading=h.16u3o9piptvm) it seems that you work within a VM when making Docker images on a Mac (although this is no longer required in the latest Docker release - https://docs.docker.com/engine/installation/mac/ - is this required if I want to call containers inside a WDL program? Said another way, is it possible to use containers made on a Mac within a WDL program from the standard Mac terminal? In turn, are there substantial changes to these programs needs before they can be deployed on a cluster?
In general, any help using WDL to write pipelines using Docker containers holding needed functions (bwa, picard, GATK) that can be developed and executed locally on a mac and ported easily to a cluster computing environment would be really helpful!