From a7a504e4a3589787d8c25c5ca97149598b65f572 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Fri, 24 Sep 2021 17:01:47 +0200
Subject: [PATCH] adjust resource settings
---
gridss.wdl | 8 ++++----
hmftools.wdl | 4 ++--
peach.wdl | 4 ++--
3 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/gridss.wdl b/gridss.wdl
index fcfed09..03193cc 100644
--- a/gridss.wdl
+++ b/gridss.wdl
@@ -94,7 +94,7 @@ task GRIDSS {
File? gridssProperties
Int jvmHeapSizeGb = 64
- Int threads = 4
+ Int threads = 8
Int timeMinutes = ceil(4320 / threads) + 10
String dockerImage = "quay.io/biocontainers/gridss:2.12.0--h270b39a_1"
}
@@ -163,10 +163,10 @@ task GridssAnnotateVcfRepeatmasker {
File gridssVcfIndex
String outputPath = "./gridss.repeatmasker_annotated.vcf.gz"
- String memory = "50G"
- Int threads = 4
+ String memory = "25G"
+ Int threads = 8
String dockerImage = "quay.io/biocontainers/gridss:2.12.0--h270b39a_1"
- Int timeMinutes = 2880
+ Int timeMinutes = 1440
}
command {
diff --git a/hmftools.wdl b/hmftools.wdl
index 199d7d8..f8b13c6 100644
--- a/hmftools.wdl
+++ b/hmftools.wdl
@@ -799,10 +799,10 @@ task Sage {
String? mnvFilterEnabled
File? coverageBed
- Int threads = 2
+ Int threads = 4
String javaXmx = "50G"
String memory = "60G"
- Int timeMinutes = 1 + ceil(size(select_all([tumorBam, normalBam]), "G") * 8 / threads)
+ Int timeMinutes = 1 + ceil(size(select_all([tumorBam, normalBam]), "G") * 9 / threads)
String dockerImage = "quay.io/biocontainers/hmftools-sage:2.8--hdfd78af_0"
}
diff --git a/peach.wdl b/peach.wdl
index b57842f..af44dae 100644
--- a/peach.wdl
+++ b/peach.wdl
@@ -30,9 +30,9 @@ task Peach {
String outputDir = "./peach"
File panelJson
- String memory = "8G"
+ String memory = "2G"
String dockerImage = "quay.io/biowdl/peach:v1.0"
- Int timeMinutes = 20
+ Int timeMinutes = 5
}
command {
--
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