The current version of this pipeline pulls the Docker image from a public AWS Elastic Container Registry. If you prefer to pull from Docker Hub (DH), please use the tagged version utilizing DH: v1.2_DH.
This repo contains the source files for a docker image stored in both 4dndcic/4dn-re-checker:v1.2 and AWS public.ecr.aws/dcic-4dn/4dn-re-checker:v1.2.
docker build -t 4dndcic/4dn-re-checker:v1.2 .
docker push 4dndcic/4dn-re-checker:v1.2
Tool wrappers are located in the scripts directory and given names of the format run-[*].sh. These wrappers are copied to the docker image at build time.
Runs 4DN-REcount.pl. Used by RE-checker.cwl
run-checker.sh -bam <bam_file> <optional_flags>