memory and runtime adjustements

bcftools.wdl

@@ -47,8 +47,8 @@ task Annotate {
         File? samplesFile        
         
         Int threads = 0
-        String memory = "256M"
-        Int timeMinutes = 10 + ceil(size(inputFile, "G"))
+        String memory = "5G"
+        Int timeMinutes = 60 + ceil(size(inputFile, "G"))
         String dockerImage = "quay.io/biocontainers/bcftools:1.10.2--h4f4756c_2"
     }
 

gridss.wdl

@@ -36,7 +36,7 @@ task GRIDSS {
         File? blacklistBed
         File? repeatmaskerBed
 
-        Int jvmHeapSizeGb = 30
+        Int jvmHeapSizeGb = 64
         Int threads = 4
         Int timeMinutes = ceil(5760 / threads) + 10
         String dockerImage = "quay.io/biocontainers/gridss:2.9.4--0"
@@ -70,7 +70,7 @@ task GRIDSS {
 
     runtime {
         cpu: threads
-        memory: "~{jvmHeapSizeGb + 1}G"
+        memory: "~{jvmHeapSizeGb + 25}G"
         time_minutes: timeMinutes # !UnknownRuntimeKey
         docker: dockerImage
     }

hmftools.wdl

@@ -35,8 +35,8 @@ task Amber {
         File referenceFastaDict
 
         Int threads = 2
-        String memory = "33G"
-        String javaXmx = "32G"
+        String memory = "52G"
+        String javaXmx = "50G"
         Int timeMinutes = 1200
         String dockerImage = "quay.io/biocontainers/hmftools-amber:3.5--0"
     }
@@ -341,7 +341,7 @@ task Linx {
         File svVcf
         File svVcfIndex
         Array[File]+ purpleOutput
-        File referenceFasta
+        File referenceFasta #FIXME Not used in pipeline5?
         File referenceFastaFai
         File referenceFastaDict
         String refGenomeVersion
@@ -597,8 +597,8 @@ task Sage {
         File? coverageBed
 
         Int threads = 2
-        String javaXmx = "32G"
-        String memory = "33G"
+        String javaXmx = "50G"
+        String memory = "75G"
         Int timeMinutes = 1 + ceil(size(select_all([tumorBam, normalBam]), "G") * 10 / threads) #FIXME make sure this is enough
         String dockerImage = "quay.io/biocontainers/hmftools-sage:2.6--0"
     }

sambamba.wdl

@@ -69,7 +69,7 @@ task Markdup {
         String outputPath
         Int compressionLevel = 1
         # sortBufferSize and ioBufferSize taken from markdup defaults as of sambamba 0.7.1.
-        Int sortBufferSize = 2048
+        Int sortBufferSize = 4096
         Int ioBufferSize = 128
         Boolean removeDuplicates = false
 
@@ -81,8 +81,8 @@ task Markdup {
         # 2 threads reduces wall clock time by more than 40%.
         Int threads = 2
         # According to the manual sambamba markdup uses the sortbufferSize + 2 times the ioBuffer size.
-        # Added 2024 mb as a margin of safety. Real life use with this setting uses 2.7 GiB.
-        Int memoryMb = 2048 + sortBufferSize + 2 * ioBufferSize
+        # Added 4096 mb as a margin of safety. Real life use with this setting uses 2.7 GiB.
+        Int memoryMb = 4096 + sortBufferSize + 2 * ioBufferSize
         # Time minute calculation does not work well for higher number of threads.
         Int timeMinutes = 1 + ceil(size(inputBams, "G") * 40) / threads
         String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"