cromwell-kccg-mutect2
Run the KCCG GATK4 Mutect2 somatic variant calling pipeline using the Cromwell workflow engine.
Usage:
Configuring MySQL server
If there is no MySQL server currently running on the cluster, run the following commands:
# Choose an empty port number.
MYSQL=/home/glsai/mysql/mysql-5.7.27-linux-glibc2.12-x86_64/
MYSQL_RUNDIR=/home/glsai/mysql/mysql-5.7.27-linux-glibc2.12-x86_64/
sqlport=40008
screen -S MySQLPort${sqlport}
# Unfortunately have to run thes
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<small>This is a companion discussion topic for the original entry at <a href='https://dockstore.org/workflows/github.com/mgeaghan-garvan/cromwell-kccg-mutect2-chip/cromwell-kccg-mutect2-batch'>github.com/mgeaghan-garvan/cromwell-kccg-mutect2-chip/cromwell-kccg-mutect2-batch</a></small>