From 9249f3e2a2265e5f7d81e1df1a9c19a25fab4391 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 23 Jul 2018 13:25:32 +0200
Subject: [PATCH] flash to 1.0
---
flash.wdl | 42 +++++++++++++++++++++++-------------------
1 file changed, 23 insertions(+), 19 deletions(-)
diff --git a/flash.wdl b/flash.wdl
index c081d49..93ba4cd 100644
--- a/flash.wdl
+++ b/flash.wdl
@@ -1,27 +1,31 @@
+version 1.0
+
task flash {
- String? preCommand
- File inputR1
- File inputR2
- String outdirPath
- String? outPrefix = "flash"
- Int? minOverlap
- Int? maxOverlap
- Boolean? compress = true
- Int? threads
- Int? memory
+ input {
+ String? preCommand
+ File inputR1
+ File inputR2
+ String outdirPath
+ String? outPrefix = "flash"
+ Int? minOverlap
+ Int? maxOverlap
+ Boolean? compress = true
+ Int? threads
+ Int? memory
+ }
command {
set -e -o pipefail
- mkdir -p ${outdirPath}
- ${preCommand}
+ mkdir -p ~{outdirPath}
+ ~{preCommand}
flash \
- ${"--threads=" + threads} \
- ${"--output-directory=" + outdirPath} \
- ${"--output-prefix=" + outPrefix} \
- ${true="--compress " false="" defined(compress)} \
- ${"--min-overlap=" + minOverlap} \
- ${"--max-overlap=" + maxOverlap} \
- ${inputR1} ${inputR2}
+ ~{"--threads=" + threads} \
+ ~{"--output-directory=" + outdirPath} \
+ ~{"--output-prefix=" + outPrefix} \
+ ~{true="--compress " false="" defined(compress)} \
+ ~{"--min-overlap=" + minOverlap} \
+ ~{"--max-overlap=" + maxOverlap} \
+ ~{inputR1} ~{inputR2}
}
output {
--
GitLab