Overview - Base
The CGAP Pipelines base module (https://github.com/dbmi-bgm/cgap-pipeline-base) contains the CWL description files, Dockerfiles, Workflow, MetaWorkflow and other shared CGAP Portal objects necessary to run general pipelines (e.g., MD5 Hash and FastQC) and format conversions (e.g., cram or bam to paired-end fastq files).
This module is necessary for general CGAP Portal functionality and should always be included when deploying pipelines to a new account.
Docker Images
The Dockerfiles provided in this GitHub repository can be used to build public docker images.
If built through portal-pipeline-utils pipeline_deploy command (https://github.com/dbmi-bgm/portal-pipeline-utils), private ECR images will be created for the target AWS account.
The md5 image contains (but is not limited to) the following software packages:
- md5sum (8.25)
The fastqc image contains (but is not limited to) the following software packages:
- fastqc (0.11.9)
The base image contains (but is not limited to) the following software packages:
- samtools (1.9)
- cramtools (0b5c9ec)
- bcftools (1.11)
- pigz (2.6)
- pbgzip (2b09f97)
The gatk_picard image contains (but is not limited to) the following software packages:
- gatk4 (4.2.6.1)
- picard (2.26.11)
The granite image contains (but is not limited to) the following software packages:
- granite-suite (0.2.0)
