fix(Manta): custom variables

tasks/Manta.wdl

     
     MANTA_INSTALL_PATH="/opt/manta-1.6.0.centos6_x86_64"
     MANTA_ANALYSIS_PATH="/cromwell_root/tmp"
-		mkdir -p ${MANTA_ANALYSIS_PATH}
+		mkdir -p $MANTA_ANALYSIS_PATH
     
     # input files
     if [ ${normal_bam} ]; then
       INPUT="--tumorBam ${tumor_bam}"
     fi
     # configManta
-    ${MANTA_INSTALL_PATH}/bin/configManta.py \
+    $MANTA_INSTALL_PATH/bin/configManta.py \
     $INPUT \
     --callRegions ${regions} --exome \
     --referenceFasta ${ref_dir}/${fasta} \
-    --runDir ${MANTA_ANALYSIS_PATH}
+    --runDir $MANTA_ANALYSIS_PATH
     # runWorkflow
-    ${MANTA_ANALYSIS_PATH}/runWorkflow.py -j $nt
+    $MANTA_ANALYSIS_PATH/runWorkflow.py -j $nt
     # results
     if [ ${normal_bam} ]; then
-      cp ${MANTA_ANALYSIS_PATH}/results/variants/somaticSV.vcf.gz ${sample}.Manta.somaticSV.vcf.gz
-      cp ${MANTA_ANALYSIS_PATH}/results/variants/diploidSV.vcf.gz ${sample}.Manta.germlineSV.vcf.gz
+      cp $MANTA_ANALYSIS_PATH/results/variants/somaticSV.vcf.gz ${sample}.Manta.somaticSV.vcf.gz
+      cp $MANTA_ANALYSIS_PATH/results/variants/diploidSV.vcf.gz ${sample}.Manta.germlineSV.vcf.gz
     else
-      cp ${MANTA_ANALYSIS_PATH}/results/variants/tumorSV.vcf.gz ${sample}.Manta.somaticSV.vcf.gz
+      cp $MANTA_ANALYSIS_PATH/results/variants/tumorSV.vcf.gz ${sample}.Manta.somaticSV.vcf.gz
     fi
 	>>>