Fix CNV pipeline

snakecnv/bin/cnvpipeline.sh

@@ -67,7 +67,10 @@ export LD_LIBRARY_PATH=/SGE/ogs/lib/linux-x64:$LD_LIBRARY_PATH
 mx="-Xmx4g"
 classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"
 
-echo "-- Run CNVPipeline -- " 
+echo "-- Run CNVPipeline -- "
+
+if [ -n "$SV_PARALLEL_DRMAA" ] && [ "$SV_PARALLEL_DRMAA" -eq "1" ]; then
+
 LC_ALL=C java -cp ${classpath} ${mx} \
     org.broadinstitute.gatk.queue.QCommandLine \
     -S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q \
@@ -80,7 +83,36 @@ LC_ALL=C java -cp ${classpath} ${mx} \
     -jobRunner Drmaa \
     -gatkJobRunner Drmaa \
     -jobQueue workq \
-    -jobNative '-l mem=16G -l h_vmem=16G' \
+    -jobNative "${SV_PARALLEL_NATIVES}" \
+    -R ${reference_prefix}.fasta \
+    -genderMaskBedFile  ${reference_prefix}.gendermask.bed \
+    -genomeMaskFile     ${reference_prefix}.svmask.fasta \
+    -genderMapFile      ${gendermap} \
+    -ploidyMapFile      ${reference_prefix}.ploidymap.txt \
+    -md ${metadata} \
+    -runDirectory ${runDir} \
+    -jobLogDir ${runDir}/logs \
+    -I ${inputFile} \
+    -intervalList $intervallist \
+    -tilingWindowSize 5000 \
+    -tilingWindowOverlap 2500 \
+    -maximumReferenceGapLength 2500 \
+    -boundaryPrecision 200 \
+    -minimumRefinedLength 2500 \
+    -run \
+    || exit 1
+
+else
+
+LC_ALL=C java -cp ${classpath} ${mx} \
+    org.broadinstitute.gatk.queue.QCommandLine \
+    -S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q \
+    -S ${SV_DIR}/qscript/SVQScript.q \
+    -cp ${classpath} \
+    -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
+    -configFile ${SV_DIR}/conf/genstrip_parameters.txt \
+    --disableJobReport \
+    -jobProject Capri \
     -R ${reference_prefix}.fasta \
     -genderMaskBedFile  ${reference_prefix}.gendermask.bed \
     -genomeMaskFile     ${reference_prefix}.svmask.fasta \
@@ -99,6 +131,8 @@ LC_ALL=C java -cp ${classpath} ${mx} \
     -run \
     || exit 1
 
+fi
+
 sites=${runDir}/results/gs_cnv.genotypes.vcf.gz
 genotypes=${outdir}/${outprefix}.vcf.gz