Running job arrays on HPC using Singularity and a Docker image
I thought I’d share a little success story. A researcher recently approached me to say he’d been having difficulty getting his bioinformatics workflow (based on this) working on the University of Sheffield’s ShARC HPC cluster and had an urgent need to get it running to meet a pending deadline. He’s primarily using the GATK ‘genome analysis toolkit’. He appealed for help on the GATK forum, members of which suggested that the issue may be due to the way in which GATK was installed.