Fixing cleanup call for --qc flag and RG name

    load_bwa="spack load bwa@0.7.17 arch=\`spack arch\`"

    load_awk="spack load gawk@4.1.4 arch=\`spack arch\`"

    load_gpu="spack load cuda@8.0.61 arch=\`spack arch\` && CUDA_VISIBLE_DEVICES=0,1,2,3"

    load_samtools="spack load samtools arch=\`spack arch\`"

    load_samtools="spack load samtools@1.13 arch=\`spack arch\`"

    call_bwameth="/gpfs0/home/neva/bwa-meth/bwameth.py"

    # Juicer directory, contains scripts/, references/, and restriction_sites/

    # can also be set in options via -D

	# RG group; ID derived from paired-end name, sample and library can be user set

	if [ $singleend -eq 1 ]

	then

	    rg="@RG\\tID:${jname%.fastq*}\\tSM:${sampleName}\\tLB:${libraryName}"

	    rg="@RG\\tID:${jname%%.fastq*}\\tSM:${sampleName}\\tLB:${libraryName}"

	else

	    rg="@RG\\tID:${jname%.fastq*}\\tSM:${sampleName}\\tPL:ILM\\tLB:${libraryName}"

	    rg="@RG\\tID:${jname%%.fastq*}\\tSM:${sampleName}\\tPL:ILM\\tLB:${libraryName}"

	fi

	touchfile=${tmpdir}/${jname}

	if [ -z "$chimeric" ]

ARROWS`

    dependarrows="#SBATCH -d ${dependhiccups}:$jid"

else

    dependarrows=""

    dependarrows=${sbatch_wait}

fi

if [ "$qc_apa" = 1 ]