Purpose

• This PR enables the Docker container that executes the CWL workflow to use the EFS /scratch directory to store temporary output, so that the workflow doesn't crash because of running out of disk space. There are also some other stylistic improvements for the current version of the SBG DAGs.

Proposed Changes

• [ADD] cwl-runner uses --tmp-outdir-prefix to create all temporary files in the EFS /scratch directory.

Issues

• [New Feature]: Execution of additional SBG workflows #40

Testing

• Executed SBG Preprocess workflow to completion using the "cwl-dag" DAG
• SBG end-to-end workflow starts correctly using the /scratch directory, but eventually fails in the ISOFIT step because of not enough memory. Currently trying again with bigger EC2s.