From e3a3add789a4a42c5acd40c38e2b654162893c32 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 29 Jun 2020 15:01:20 +0200
Subject: [PATCH] fix sambamba threads
---
sambamba.wdl | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/sambamba.wdl b/sambamba.wdl
index 1b10b37..3337773 100644
--- a/sambamba.wdl
+++ b/sambamba.wdl
@@ -26,7 +26,7 @@ task Markdup {
Array[File] inputBams
String outputPath
# Sambamba additional threads like samtools
- Int threads = 0
+ Int threads = 1
Int compressionLevel = 1
Int? hashTableSize
Int? overFlowListSize
@@ -64,7 +64,7 @@ task Markdup {
runtime {
memory: "~{memoryGb}G"
- cpu: threads + 1
+ cpu: threads
time_minutes: timeMinutes
docker: dockerImage
}
@@ -77,9 +77,9 @@ task Sort {
Boolean sortByName = false
Int compressionLevel = 1
# Sambamba additional threads like samtools
- Int threads = 0
+ Int threads = 1
Int memoryPerThreadGb = 4
- Int memoryGb = 1 + (threads + 1) * memoryPerThreadGb
+ Int memoryGb = 1 + threads * memoryPerThreadGb
String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
Int timeMinutes = 1 + ceil(size(inputBam, "G") * 3)
}
@@ -107,7 +107,7 @@ task Sort {
}
runtime {
- cpu: threads + 1
+ cpu: threads
memory: "~{memoryGb}G"
docker: dockerImage
time_minutes: timeMinutes
--
GitLab