Merge pull request #130 from Amfgcp/fixes-run-shark

update to run in Shark: memory values and no "-o pipefail"

gatk.wdl

@@ -331,8 +331,8 @@ task MergeStats {
     input {
         Array[File]+ stats
 
-        Int memory = 2
-        Float memoryMultiplier = 1.5
+        Int memory = 14
+        Float memoryMultiplier = 2
         String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
     }
 
@@ -435,7 +435,7 @@ task FilterMutectCalls {
         File mutect2Stats
         String? extraArgs
 
-        Int memory = 4
+        Int memory = 8
         Float memoryMultiplier = 1.5
         String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
     }
@@ -558,4 +558,4 @@ task CombineVariants {
         docker: dockerImage
         memory: ceil(memory * memoryMultiplier)
     }
-}
\ No newline at end of file
+}

somaticseq.wdl

@@ -280,7 +280,7 @@ task ModifyStrelka {
     }
 
     command {
-        set -e -o pipefail
+        set -e
 
         ~{installDir}/modify_Strelka.py \
         -infile ~{strelkaVCF} \