Previously, multi sample calling was done on the merged per sample g.vcf
files. However, in rare cases, VCF files that are merged by bcftools can
trigger a crash in GATK.

To resolve this, the multi sample calling now uses the scattered per
sample g.vcf files, so that GATK does not have to act on VCF files that
were modified by bcftools.

As an added advantage, using the scatters directly for the multi sample
calling allows for better parallelisation.

Full rewrite of the pipeline

Merge latest changes and testing into develop

Add github workflow testing

This reverts commit fb607603.

MultiQC can run out of /tmp space on execution nodes on shark, leading
to incorrect results or crashes. This commit fixes this problem by
specifying a default location for the python tempfiles that MultiQC uses
via the environment variable TMPFILE inside of the shell block for the
MultiQC rule.