This repository contains all of the WDL-based bioinformatic workflows and tasks created by\nMass General Brigham Personalized Medicine for processing genomic data. It also contains\nutility and orchestration tasks. The reusable steps and workflows are organized into a\ndirectory structure, outlined below by way of example:
\nsteps/ - Contains all re-usable workflow steps, which may be WDL tasks and workflows\n ...wdls - WDL files, with one workflow and/or many tasks per file\n ...mds - Workflow and task documentation files, one for each WDL file\nworkflows/ - Contains one sub-directory for each MGBPM workflow\n wgs_b38/ - Contains all artifacts for the workflow\n WGSSingleSampleBuild38.wdl - The workflow definition\n WGSSingleSampleBuild38.md - Workflow documentation, especially inputs and outputs\n prs_b38/\n ...similar to wgs...\n.dockstore.yml - File that defines all the workflows to be imported by Dockstore\nALL CONTENTS OF THIS REPOSITORY WILL BE PUBLISHED ON GITHUB
\nCREDENTIALS OR OTHER CONFIDENTIAL INFORMATION ARE STRICTLY FORBIDDEN
\nThe following guidelines should be followed for WDL development:
\ngcr.io/mgb-lmm-gcp-infrast-1651079146/mgbpmbiofx/base:latestWhen workflow WDLs are ready for production use, the relevant commit will be tagged with workflow specific tags to avoid collisions. For example, WGSSingleSampleBuild38_2.5.0. Versioning for workflow WDLs should adhere to the principles of semantic versioning.
The master copy of this repository is hosted in Azure DevOps. All new content is mirrored to GitHub and workflows subsequently published in Dockstore.
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