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@@ -7,7 +7,7 @@ This repository contains components for the CGAP pipeline for Structural Variant
* CWL workflow descriptions
* CGAP Portal *Workflow* and *MetaWorkflow* objects
* CGAP Portal *Software*, *FileFormat*, and *FileReference* objects
* ECR (Docker) source files, which allow for creation of public Docker images (using `docker build`) or private dynamically-generated ECR images (using [*cgap pipeline utils*](https://github.com/dbmi-bgm/cgap-pipeline-utils/)`pipeline_deploy`)
* ECR (Docker) source files, which allow for creation of public Docker images (using `docker build`) or private dynamically-generated ECR images (using [*portal pipeline utils*](https://github.com/dbmi-bgm/portal-pipeline-utils/)`pipeline_deploy`)
The pipeline starts from analysis-ready `bam` files and produces `vcf` files containing calls for SVs as output.
Documentation for all CGAP Pipelines can now be found here:
