From 0665c22fa2d64813c022e3e9dc731dac2a5fa63c Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 24 Jun 2020 13:25:52 +0200
Subject: [PATCH] Add sortSam task
---
picard.wdl | 46 ++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 46 insertions(+)
diff --git a/picard.wdl b/picard.wdl
index 0ee5da3..ef648ae 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -650,6 +650,52 @@ task ScatterIntervalList {
}
}
+task SortSam {
+ input {
+ File inputBam
+ String outputPath
+
+ Int XmxGb = 4
+ Int memoryGb = 1 + XmxGb
+ Int timeMinutes = 1 + ceil(size(inputBam, "G") * 2)
+ # A mulled container is needed to have both picard and bwa in one container.
+ # This container contains: picard (2.18.7), bwa (0.7.17-r1188)
+ String dockerImage = "quay.io/biocontainers/picard:2.23.1--h37ae868_0"
+ }
+
+ command {
+ mkdir -p "$(dirname ~{outputPath})"
+ picard -Xmx~{XmxGb}G -XX:ParallelGCThreads=1 SortSam \
+ INPUT=/dev/stdin \
+ OUTPUT=~{outputPath} \
+ SORT_ORDER=coordinate \
+ CREATE_INDEX=true
+ }
+
+ output {
+ File outputBam = outputPath
+ File outputBamIndex = sub(outputPath, "\.bam$", ".bai")
+ }
+
+ runtime {
+ cpu: 1
+ memory: "~{memoryGb}G"
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ inputBam: {description: "The unsorted input BAM file", category: "required"}
+ outputPath: {description: "The location the output BAM file should be written to.", category: "required"}
+ memoryGb: {description: "The amount of memory this job will use.", category: "advanced"}
+ XmxGb: {description: "The maximum memory available to picard SortSam. Should be lower than `memory` to accommodate JVM overhead and BWA mem's memory usage.",
+ 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"}
+ }
+}
+
task SortVcf {
input {
Array[File]+ vcfFiles
--
GitLab