add index for commonvariantsites (CollectAllelicounts)

BIOWDL-386: Fix issue where Centrifuge could not locate index files.

increase default memory for BWA mem

make memory configurable in fastqc

BIOWDL-386: Fix issue where centrifuge would fail on incorrect paths.

Add tasks for GATK CNV calling

Add bedtools intersect and text to file task.

BIOWDL-386: Centrifuge should use -U instead of -1 with single end data.