From 5b096cee1b35d8ff404567571ce429f3a46ec7c4 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 24 Jun 2020 10:43:27 +0200
Subject: [PATCH] Put sorting back into bwakit task
---
bwa.wdl | 20 +++++++++++++++++---
1 file changed, 17 insertions(+), 3 deletions(-)
diff --git a/bwa.wdl b/bwa.wdl
index 3e11eb2..0095f48 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -92,7 +92,16 @@ task Kit {
Boolean sixtyFour = false
Int threads = 4
- String memoryGb = 1 + ceil(size(bwaIndex.indexFiles, "G"))
+
+ # Samtools uses *additional* threads. So by default this option should
+ # not be used.
+ Int sortThreads = 0
+ # 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
Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 220 / threads)
String dockerImage = "biowdl/bwakit:0.7.17-dev-experimental"
}
@@ -112,7 +121,7 @@ task Kit {
~{bwaIndex.fastaFile}~{true=".64.alt" false=".alt" sixtyFour} | \
samtools sort \
~{"-@ " + sortThreads} \
- -m ~{sortMemoryPerThread} \
+ -m ~{sortMemoryPerThreadGb}G \
-l ~{compressionLevel} \
- \
-o ~{outputPrefix}.aln.bam
@@ -121,6 +130,7 @@ task Kit {
output {
File outputBam = outputPrefix + ".aln.bam"
+ File outputBamIndex = outputPrefix + ".aln.bai"
}
runtime {
@@ -141,14 +151,18 @@ task Kit {
readgroup: {description: "A readgroup identifier.", category: "common"}
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"}
+ 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"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
# outputs
outputBam: "The produced BAM file."
+ outputBamIndex: "The index of the produced BAM file."
}
}
--
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