adding abra2

alignment/abra2.sh

+#!/bin/bash
+#gatkrunner.sh
+
+usage() {
+  echo "-h Help documentation for gatkrunner.sh"
+  echo "-r  --Reference Genome: GRCh38 or GRCm38"
+  echo "-b  --BAM File"
+  echo "-p  --Prefix for output file name"
+  echo "-a  --Algorithm/Command"
+  echo "Example: bash hisat.sh -p prefix -r GRCh38 -b File.bam"
+  exit 1
+}
+OPTIND=1 # Reset OPTIND
+while getopts :r:a:c:b:p:h opt
+do
+    case $opt in
+        r) index_path=$OPTARG;;
+        b) sbam=$OPTARG;;
+        p) pair_id=$OPTARG;;
+	c) tbed==$OPTARG;;
+        h) usage;;
+    esac
+done
+
+shift $(($OPTIND -1))
+
+# Check for mandatory options
+if [[ -z $pair_id ]] || [[ -z $sbam ]] || [[ -z $index_path ]]
+then
+    usage
+fi
+
+NPROC=$SLURM_CPUS_ON_NODE
+if [[ -z $NPROC ]]
+then
+    NPROC=`nproc`
+fi
+
+if [[ -z $isdocker ]]
+then
+    source /etc/profile.d/modules.sh
+    module load abra2/2.18 samtools/gcc/1.8
+    abrajar=/cm/shared/apps/abra2/lib/abra2.jar
+else
+    abrajar=/usr/local/bin/abra2.jar
+fi
+ioopt="--in ${sbam} --out ${pair_id}.abra2.bam"
+opt=''
+if [ -n "$tbed" ]
+then
+    opt="--targets $tbed"
+fi
+
+which samtools
+samtools index -@ $NPROC ${sbam}
+mkdir tmpdir
+java -Xmx16G -jar ${abrajar} ${ioopt} --ref ${index_path}/genome.fa --threads $NRPOC $opt --tmpdir tmpdir --mbq 150 --mnf 5 --mer 0.05 > abra.log
+samtools index -@ $NPROC ${pair_id}.abra2.bam