From a0de5e64323c47a390851719af2781f4096ddb9f Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 19 Jun 2018 14:30:32 +0200
Subject: [PATCH] add validatefastq
---
biopet.wdl | 24 ++++++++++++++++++++++++
1 file changed, 24 insertions(+)
diff --git a/biopet.wdl b/biopet.wdl
index 286b2e0..b6fa893 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -305,3 +305,27 @@ task Seqstat {
}
}
+task ValidateFastq {
+ String? preCommand
+ File? toolJar
+ File fastq1
+ File? fastq2
+
+ 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-validatefastq -Xmx" + mem + "G"
+
+ command {
+ set -e -o pipefail
+ ${preCommand}
+ biopet-validatefastq \
+ --fastq1 ${fastq1} \
+ ${"--fastq2 " + fastq2}
+ }
+
+}
+
--
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