From fbc7b95956624b01e0e60574e18f6849cc149976 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 26 Jun 2020 14:31:02 +0200
Subject: [PATCH] proper threads for sambamba
---
sambamba.wdl | 15 +++++++++------
1 file changed, 9 insertions(+), 6 deletions(-)
diff --git a/sambamba.wdl b/sambamba.wdl
index 4de4dfd..1b10b37 100644
--- a/sambamba.wdl
+++ b/sambamba.wdl
@@ -25,7 +25,8 @@ task Markdup {
input {
Array[File] inputBams
String outputPath
- Int threads = 1
+ # Sambamba additional threads like samtools
+ Int threads = 0
Int compressionLevel = 1
Int? hashTableSize
Int? overFlowListSize
@@ -52,7 +53,8 @@ task Markdup {
~{"--sort-buffer-size " + sortBufferSize} \
~{"--io-buffer-size " + ioBufferSize} \
~{sep=' ' inputBams} ~{outputPath}
- sambamba index ~{outputPath} ~{bamIndexPath}
+ # sambamba creates an index for us
+ mv ~{outputPath}.bai ~{bamIndexPath}
}
output {
@@ -62,7 +64,7 @@ task Markdup {
runtime {
memory: "~{memoryGb}G"
- cpu: threads
+ cpu: threads + 1
time_minutes: timeMinutes
docker: dockerImage
}
@@ -74,9 +76,10 @@ task Sort {
String outputPath = basename(inputBam, "\.bam") + ".sorted.bam"
Boolean sortByName = false
Int compressionLevel = 1
- Int threads = 1
+ # Sambamba additional threads like samtools
+ Int threads = 0
Int memoryPerThreadGb = 4
- Int memoryGb = 1 + threads * memoryPerThreadGb
+ Int memoryGb = 1 + (threads + 1) * memoryPerThreadGb
String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
Int timeMinutes = 1 + ceil(size(inputBam, "G") * 3)
}
@@ -104,7 +107,7 @@ task Sort {
}
runtime {
- cpu: threads
+ cpu: threads + 1
memory: "~{memoryGb}G"
docker: dockerImage
time_minutes: timeMinutes
--
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