StaticSection Source Files

The CUT&RUN pipeline is separated into two types of workflows: (1) The alignment workflow for control and experimental data and (2) the peak-calling workflow.

For the current version (v1), the Docker image source code and pipeline description in Common Workflow Language (CWL) are available on GitHub:

• CWL: https://github.com/4dn-dcic/docker-4dn-cut-and-run-pipeline/tree/v1/cwl
• Docker: https://github.com/4dn-dcic/docker-4dn-cut-and-run-pipeline/tree/v1/
• Scripts (also in the Docker image): https://github.com/4dn-dcic/docker-4dn-cut-and-run-pipeline/tree/v1/scripts

CUT&RUN QC metrics will be available in the next version of the pipeline.