def gatk_contig_check():
    """ For Gatk contig style wrappers. Will create a bash sctring to
    determine if the contig is 'unmapped' and if so will set the contig
    param accordingly """
    return """# Check for the unmapped as the contig
# If not, write no_mapped_reads to outBam
if [ "$contig" == "unmapped" ]; then
	contigParam=""
else
	contigParam="-L $contig"
fi"""
