Orchestrate workflows with CWL - MaastrichtU-IDS/data2services-pipeline GitHub Wiki

The Common Workflow Language can be used to define workflows of Docker containers from the Data2Services ecosystem.

At the moment we will use the cwltool reference implementation on Ubuntu. Feel free to use your favorite implementation of CWL.

sudo apt install cwltool

cwl-runner documentation

• Run in Docker
• Docker additional param for Java
• Environment variable
• Writing workflows
• Nested workflows
• Metadata and ontology in CWL

Dockstore

Developed by the Cancer Genome Collaboratory, it is an open platform used by the GA4GH for sharing Docker-based tools described with the Common Workflow Language (CWL), the Workflow Description Language (WDL), or Nextflow (NFL)

• Dockstore CWL documentation
• Example of Dockstore Workflow with 2 docker container chained with output/input
• Install Dockstore CLI
• Extended metadata for Dockstore

Rabix Composer

Graphical UI to build CWL Workflows. See on GitHub