The Snakefile is adapted to run inside a singularity container built with singularity version 2.5.1, build the image with the BuildSingularityImage.sh script. It uses the oskarv/snakemake-germline-tools docker image to build the singularity image. It is not possible to download a prebuilt singularity image.
Edit ./start-workflow.sh and change the file path for REFERENCES to the filepath where the reference files are stored. In order to support more than one reference file version the file path needs to be of this format: /storage/workflows/references/, and in the references folder there should be a directory called hg38 and a directory called b37. The config file has file paths for. Use these links to download b37 and hg38 reference files from Googles cloud, a Google account is necessary to access the links.
There is also a public ftp server here: ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle
There is no password.
Use this command to automatically download the hg38 folder:
wget -m ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38
The wgs interval list for b37 isn't available on the ftp so use the google link above to download that as well. The hg38 bundle on the ftp is complete.
Index the fasta file with bwa before running the pipeline like so: bwa index -a bwtsw hg38.fasta.