From 321d6d9441ad941355e96fc9d6de3dfebbd5b737 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 20 Aug 2018 15:31:53 +0200
Subject: [PATCH] fix seqstats
---
biopet/seqstat.wdl | 16 ++++++++++------
1 file changed, 10 insertions(+), 6 deletions(-)
diff --git a/biopet/seqstat.wdl b/biopet/seqstat.wdl
index 2009975..959d9ef 100644
--- a/biopet/seqstat.wdl
+++ b/biopet/seqstat.wdl
@@ -1,13 +1,17 @@
+version 1.0
+
+# Copyright Sequencing Analysis Support Core - Leiden University Medical Center 2018
+
task Generate {
input {
String? preCommand
File? toolJar
File fastqR1
- File fastqR2
+ File? fastqR2
String outputFile
- String? sample
- String? library
- String? readgroup
+ String sample = "sample"
+ String library = "library"
+ String readgroup = "readgroup"
Int memory = 4
Float memoryMultiplier = 2.0
@@ -21,9 +25,9 @@ task Generate {
set -e -o pipefail
~{preCommand}
mkdir -p $(dirname ~{outputFile})
- ~{toolCommand} \
+ ~{toolCommand} Generate \
--fastqR1 ~{fastqR1} \
- --fastqR2 ~{fastqR2} \
+ ~{"--fastqR2 " + fastqR2} \
--output ~{outputFile} \
~{"--sample " + sample} \
~{"--library " + library } \
--
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