From 9bc3b50ac8b0a12525c4caeb3ad5e93437f125e4 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 14 Jun 2018 14:22:47 +0200
Subject: [PATCH] added SeqStat
---
biopet.wdl | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)
diff --git a/biopet.wdl b/biopet.wdl
index 7a16368..46f6179 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -277,6 +277,28 @@ task ScatterRegions {
}
task Seqstat {
+ String? preCommand
+ File? toolJar
+ File fastq
+ String outputFile
+ Float? memory
+ Float? memoryMultiplier
+ Int mem = ceil(select_first([memory, 4.0]))
+
+ String toolCommand = if defined(toolJar)
+ then "java -Xmx" + mem + "G -jar " +toolJar
+ else "biopet-seqstat -Xmx" + mem + "G"
+ command {
+ set -e -o pipefail
+ ${preCommand}
+ mkdir -p ${outputFile}
+ ${toolCommand} \
+ --fastq ${fastq} \
+ --output ${outputFile}
+ }
+ runtime {
+ memory: ceil(mem * select_first([memoryMultiplier, 2.0]))
+ }
}
--
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