From b92acedc9e496bb0636ec39c24fd5e81da914770 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 17 Sep 2018 17:03:06 +0200
Subject: [PATCH] switch flash to structs
---
flash.wdl | 11 ++++++++---
1 file changed, 8 insertions(+), 3 deletions(-)
diff --git a/flash.wdl b/flash.wdl
index 3d3eecd..728a237 100644
--- a/flash.wdl
+++ b/flash.wdl
@@ -1,10 +1,11 @@
version 1.0
+import "common.wdl" as common
+
task Flash {
input {
String? preCommand
- File inputR1
- File inputR2
+ FastqPair inputFastq
String outdirPath
String outPrefix = "flash"
Int? minOverlap
@@ -25,13 +26,17 @@ task Flash {
~{true="--compress " false="" compress} \
~{"--min-overlap=" + minOverlap} \
~{"--max-overlap=" + maxOverlap} \
- ~{inputR1} ~{inputR2}
+ ~{inputFastq.R1} ~{inputFastq.R2}
}
output {
File extendedFrags = outdirPath + "/" + outPrefix + ".extendedFrags.fastq.gz"
File notCombined1 = outdirPath + "/" + outPrefix + ".notCombined_1.fastq.gz"
File notCombined2 = outdirPath + "/" + outPrefix + ".notCombined_2.fastq.gz"
+ FastqPair notCombined = object {
+ R1: notCombined1,
+ R2: notCombined2
+ }
File hist = outdirPath + "/" + outPrefix + ".hist"
File histogram = outdirPath + "/" + outPrefix + ".histogram"
}
--
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