Adding WDL and Docker files and run example for Task 2.1.1 and 2.1.3

microbiomedata / WorkflowPlanning

This is primarily a repo for capturing policies and discussions around the different workflows for NMDC. This is also used for project management related pieces.

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Adding WDL and Docker files and run example for Task 2.1.1 and 2.1.3 #7

Closed chienchi closed 4 years ago

chienchi commented 4 years ago

There are three directory added for the pull request.

AssemblyPipeline
Docker
MAGsPipeline

There are corresponding README.md file for AssemblyPipeline and MAGsPipeline. The Docker directory include the Dockerfile for the container image for both pipeline.

scanon commented 4 years ago

I'm fine with merging this but I would like to eventually get all the WDL pipelines to be container runtime agnostic and that just come from the config file (e.g. the WDL wouldn't contain any shifter, charliecloud, singularity commands).