From 2e4f73df50934915b7be3bde24bb30279a8686c0 Mon Sep 17 00:00:00 2001
From: ffinfo <pjrvanthof@gmail.com>
Date: Mon, 10 Sep 2018 12:53:40 +0200
Subject: [PATCH] Switch to structs
---
biopet/seqstat.wdl | 7 +++----
1 file changed, 3 insertions(+), 4 deletions(-)
diff --git a/biopet/seqstat.wdl b/biopet/seqstat.wdl
index c1e83a2..1a1651e 100644
--- a/biopet/seqstat.wdl
+++ b/biopet/seqstat.wdl
@@ -6,8 +6,7 @@ task Generate {
input {
String? preCommand
File? toolJar
- File fastqR1
- File? fastqR2
+ FastqPair fastq
String outputFile
String sample
String library
@@ -26,8 +25,8 @@ task Generate {
~{preCommand}
mkdir -p $(dirname ~{outputFile})
~{toolCommand} Generate \
- --fastqR1 ~{fastqR1} \
- ~{"--fastqR2 " + fastqR2} \
+ --fastqR1 ~{fastq.R1} \
+ ~{"--fastqR2 " + fastq.R2} \
--output ~{outputFile} \
~{"--sample " + sample} \
~{"--library " + library } \
--
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