From 82e9c135d4d5dcf7c86c8108a3a4c6d230cd3691 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 29 Jun 2020 15:15:25 +0200
Subject: [PATCH] Remove additional thread nonsense
---
bwa.wdl | 9 +++------
sambamba.wdl | 4 +---
2 files changed, 4 insertions(+), 9 deletions(-)
diff --git a/bwa.wdl b/bwa.wdl
index 8d2cb75..3b092e8 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -92,16 +92,13 @@ task Kit {
Boolean sixtyFour = false
Int threads = 4
-
- # Samtools uses *additional* threads. So by default this option should
- # not be used.
- Int sortThreads = 0
+ Int sortThreads = 1
# Compression uses zlib. Higher than level 2 causes enormous slowdowns.
# GATK/Picard default is level 2.
Int sortMemoryPerThreadGb = 4
Int compressionLevel = 1
# BWA needs slightly more memory than the size of the index files (~10%). Add a margin for safety here.
- Int memoryGb = 1 + ceil(size(bwaIndex.indexFiles, "G") * 1.2) + sortMemoryPerThreadGb * (sortThreads + 1)
+ Int memoryGb = 1 + ceil(size(bwaIndex.indexFiles, "G") * 1.2) + sortMemoryPerThreadGb * sortThreads
Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 220 / threads)
String dockerImage = "biowdl/bwakit:0.7.17-dev-experimental"
}
@@ -152,7 +149,7 @@ task Kit {
sixtyFour: {description: "Whether or not the index uses the '.64' suffixes.", category: "common"}
threads: {description: "The number of threads to use for alignment.", category: "advanced"}
memoryGb: {description: "The amount of memory this job will use in gigabytes.", category: "advanced"}
- sortThreads: {description: "The number of additional threads to use for sorting.", category: "advanced"}
+ sortThreads: {description: "The number of threads to use for sorting.", category: "advanced"}
sortMemoryPerThreadGb: {description: "The amount of memory for each sorting thread in gigabytes.", category: "advanced"}
compressionLevel: {description: "The compression level of the output BAM.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
diff --git a/sambamba.wdl b/sambamba.wdl
index 3337773..4ef62dd 100644
--- a/sambamba.wdl
+++ b/sambamba.wdl
@@ -25,7 +25,6 @@ task Markdup {
input {
Array[File] inputBams
String outputPath
- # Sambamba additional threads like samtools
Int threads = 1
Int compressionLevel = 1
Int? hashTableSize
@@ -76,7 +75,6 @@ task Sort {
String outputPath = basename(inputBam, "\.bam") + ".sorted.bam"
Boolean sortByName = false
Int compressionLevel = 1
- # Sambamba additional threads like samtools
Int threads = 1
Int memoryPerThreadGb = 4
Int memoryGb = 1 + threads * memoryPerThreadGb
@@ -122,7 +120,7 @@ task Sort {
memoryGb: {description: "The amount of memory available to the job in gigabytes.", category: "advanced"}
memoryPerThreadGb: {description: "The amount of memory used per sort thread in gigabytes", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
- threads: {description: "The number of additional threads that will be used for this task.", category: "advanced"}
+ threads: {description: "The number of threads that will be used for this task.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
# outputs
outputBam: {description: "Sorted BAM file."}
--
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