Pass R libpath to CNVkit to handle installation in non-standard directories. etal/cnvkit#2
Enable passing in GATK and MuTect jars from S3 as global resources. Download locally and link into configuration to use the remote file. Allows running GATK tools with docker containers.
Avoid re-calculating depth metrics when running post variant calling annotation with GATK to provide accurate metrics on high depth samples. Thanks to @mjafin
Initial support for downloading on-demand pre-prepared genomes from s3 on AWS