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The McDonnell Genome Institute (MGI) and collaborating labs and departments of Washington University School of Medicine share Common Workflow Language (CWL) workflow definitions focused on reusable, reproducible analysis pipelines for genomics data.
This section outlines the Whole Genome Sequencing (WGS) Clinical Assay developed at the McDonnell Genome Institute with support from the Institute of Clinical and Translational Sciences (ICTS) at WUSM.
Many pipelines have common inputs that are used throughout the repository. See Gathering input files for additional documentation on these common inputs. In addition, each tool, subworkflow and pipeline has a specific list of inputs automatically documented by the CWL descriptions of each. See the below TOC
All tools have auto-generated documentation, each page populated with the source CWL formatted documentation.
All subworkflows have auto-generated documentation, each page populated with the source CWL formatted documentation.
All pipelines have auto-generated documentation, each page populated with the source CWL formatted documentation.
Please see the FAQ for answers to common questions or submit a new Issue for assistance.