From 5893adcc35411d9f4488cea7b59b3a4c111347e0 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 7 May 2018 16:35:42 +0200
Subject: [PATCH] add picard SamToFastq
---
picard.wdl | 34 ++++++++++++++++++++++++++++++++++
1 file changed, 34 insertions(+)
diff --git a/picard.wdl b/picard.wdl
index 1042618..8177b26 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -147,6 +147,40 @@ task MergeVCFs {
File output_vcf_index = output_vcf_path + ".tbi"
}
+ runtime {
+ memory: ceil(mem * select_first([memoryMultiplier, 1.5]))
+ }
+}
+
+task SamToFastq {
+ String? preCommand
+ File inputBam
+ String outputRead1
+ String? outputRead2
+ String? outputUnpaired
+ String picard_jar
+ Float? memory
+ Float? memoryMultiplier
+ Int mem = ceil(select_first([memory, 4.0]))
+
+ command {
+ set -e -o pipefail
+ ${preCommand}
+ java \
+ -Xmx${mem}G \
+ -jar ${picard_jar} \
+ I=${inputBam} \
+ ${"FASTQ=" + outputRead1} \
+ ${"SECOND_END_FASTQ=" + outputRead2} \
+ ${"UNPAIRED_FASTQ=" + outputUnpaired}
+ }
+
+ output {
+ File read1 = outputRead1
+ File? read2 = outputRead2
+ File? unpairedRead = outputUnpaired
+ }
+
runtime {
memory: ceil(mem * select_first([memoryMultiplier, 1.5]))
}
--
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