There were some failed tests due to changes in the order of checks in
the Snakefile, which caused the wrong error to be thrown when there were
multiple missing files. This commit fixes that issue.

The KNOWN_SITES argument has been made mandatory for now, and this
requirement has also been added to the test cases.

Remove deprecated sanity checks for the GAKT jar file and the different
VCF files that are used for BQSR.
Remove the 'functional' tag since it was identical to integration.
Remove the conda specific test cases, since conda has been deprecated.

Fix picard heapspace error in align rule

See merge request !11

In the Singularity image for picard, the default heapsize is too small,
leading to crashes in the pipeline when the rule 'align' runs out of
heap space. The solution is to explicitly specify the heap space that
picard can use, thereby overriding the default value that is set in the
Singularity image.

This issue was reported on capture-lumc-wrapper, see
https://git.lumc.nl/klinische-genetica/capture-lumc/capture-lumc-wrapper/issues/26
for details.

Bcftools concat in stead of GATK catvariants

minor typo

Singularity support