adjust some runtime settings

bedtools.wdl

@@ -76,7 +76,7 @@ task Coverage {
         String outputPath = "./coverage.tsv"
 
         String memory = "8G"
-        Int timeMinutes = 120
+        Int timeMinutes = 320
         String dockerImage = "quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_2"
     }
 

gridss.wdl

@@ -93,9 +93,9 @@ task GRIDSS {
         File? blacklistBed
         File? gridssProperties
 
-        Int jvmHeapSizeGb = 300
-        Int nonJvmMemoryGb = 50
-        Int threads = 16
+        Int jvmHeapSizeGb = 64
+        Int nonJvmMemoryGb = 10
+        Int threads = 12
         Int timeMinutes = ceil(7200 / threads) + 1800
         String dockerImage = "quay.io/biowdl/gridss:2.12.2"
     }
@@ -216,9 +216,9 @@ task Virusbreakend {
         String outputPath = "./virusbreakend.vcf"
 
         String memory = "75G"
-        Int threads = 8
+        Int threads = 12
         String dockerImage = "quay.io/biowdl/gridss:2.12.2"
-        Int timeMinutes = 180
+        Int timeMinutes = 320
     }
 
     command {

hmftools.wdl

@@ -780,7 +780,7 @@ task Orange {
 
         String memory = "17G"
         String javaXmx = "16G"
-        Int timeMinutes = 1440 #FIXME
+        Int timeMinutes = 10
         String dockerImage = "quay.io/biowdl/orange:v1.6"
     }
 
@@ -1225,9 +1225,9 @@ task Sage {
         String? mnvFilterEnabled
         File? coverageBed
 
-        Int threads = 4
-        String javaXmx = "50G"
-        String memory = "51G"
+        Int threads = 32
+        String javaXmx = "120G"
+        String memory = "121G"
         Int timeMinutes = 1 + ceil(size(select_all([tumorBam, referenceBam]), "G") * 9 / threads)
         String dockerImage = "quay.io/biocontainers/hmftools-sage:2.8--hdfd78af_1"
     }

sambamba.wdl

@@ -28,7 +28,7 @@ task Flagstat {
 
         Int threads = 2
         String memory = "8G"
-        Int timeMinutes = 120
+        Int timeMinutes = 320
         String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
     }