The Common Workflow Language (CWL)
The Common Workflow Language (CWL) is emerging as a standard for defining and sharing bioinformatic workflows, and the NCI-GDC is planning to release all of its standardized workflows in this format.
In the sections below, we present a tutorial on running a sample NCI-GDC workflow with step-by-step instructions to run it on a sample input BAM file using a Google Compute Engine (GCE) VM. The second section describes how to use a convenient “helper-script” called cwl_runner (available on github) which wraps many of the individual steps required to create a GCE disk, spin up a GCE VM, mount and format the disk, etc, allowing you to run a CWL workflow in one easy step.