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.

Add bedtools tasks and add ploidity to haplotypecaller for gender aware variant-calling.

Co-Authored-By: DavyCats <davycats.dc@gmail.com>

BIOWDL-380: Update centrifuge task.