From 0862eab38451da3de6615ad419ea56402690e7a0 Mon Sep 17 00:00:00 2001
From: dcats <d.cats@lumc.nl>
Date: Mon, 12 Apr 2021 16:50:33 +0200
Subject: [PATCH] memory and runtime adjustements
---
bcftools.wdl | 4 ++--
gridss.wdl | 4 ++--
hmftools.wdl | 10 +++++-----
sambamba.wdl | 6 +++---
4 files changed, 12 insertions(+), 12 deletions(-)
diff --git a/bcftools.wdl b/bcftools.wdl
index 4827a63..28b6269 100644
--- a/bcftools.wdl
+++ b/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"
}
diff --git a/gridss.wdl b/gridss.wdl
index b4b36b0..11014a8 100644
--- a/gridss.wdl
+++ b/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
}
diff --git a/hmftools.wdl b/hmftools.wdl
index dc31f41..553879f 100644
--- a/hmftools.wdl
+++ b/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"
}
diff --git a/sambamba.wdl b/sambamba.wdl
index b4eca66..c8d9e11 100644
--- a/sambamba.wdl
+++ b/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"
--
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