Merge pull request #304 from biowdl/performance

Performance changes for WGSinCancerDiagnostics

CHANGELOG.md

@@ -9,6 +9,22 @@ that users understand how the changes affect the new version.
 -->
 version 5.1.0-dev
 ---------------------------
++ Bedtools coverage's timeMinutes now defaults to `320`.
++ Gridss' runtime attribute defaults were changed to:
+  + jvmHeapSizeGb: `64`
+  + nonJvmMemoryGb: `10`
+  + threads: `12`
++ Virusbreakend's runtime attribute defaults were changed to:
+  + threads: `12`
+  + timeMinutes: `320`
++ Cobalt's timeMinutes now defaults to `480`.
++ Orange's timeMinutes now defaults to 10.
++ Sage's runtime attributes were changed to:
+  + threads: `32`
+  + javaXmx: `"16G"`
+  + memory: `"20G"`
+  + timeMinutes: `720`
++ Sambamba's runtimeMinutes nor defaults to `320`.
 + Added a task for CupGenerateReport.
 + Updated Cuppa to version 1.6.
 + Added a task for Gripss.

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

@@ -161,9 +161,9 @@ task GRIDSS {
         File? blacklistBed
         File? gridssProperties
 
-        Int jvmHeapSizeGb = 300
-        Int nonJvmMemoryGb = 50
-        Int threads = 4
+        Int jvmHeapSizeGb = 64
+        Int nonJvmMemoryGb = 10
+        Int threads = 12
         Int timeMinutes = ceil(7200 / threads) + 1800
         String dockerImage = "quay.io/biowdl/gridss:2.12.2"
     }
@@ -290,9 +290,9 @@ 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

@@ -114,7 +114,7 @@ task Cobalt {
         Int threads = 1
         String memory = "5G"
         String javaXmx = "4G"
-        Int timeMinutes = 240
+        Int timeMinutes = 480
         String dockerImage = "quay.io/biocontainers/hmftools-cobalt:1.11--0"
     }
 
@@ -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"
     }
 
@@ -1225,10 +1225,10 @@ task Sage {
         String? mnvFilterEnabled
         File? coverageBed
 
-        Int threads = 4
-        String javaXmx = "50G"
-        String memory = "51G"
-        Int timeMinutes = 1 + ceil(size(select_all([tumorBam, referenceBam]), "G") * 9 / threads)
+        Int threads = 32
+        String javaXmx = "16G"
+        String memory = "20G"
+        Int timeMinutes = 720
         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"
     }