From 97bff342732ab5b16d8ca9342f403550996cdb0d Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 18 Apr 2018 09:41:42 +0200
Subject: [PATCH] remove poretools.wdl
---
poretools.wdl | 40 ----------------------------------------
1 file changed, 40 deletions(-)
delete mode 100644 poretools.wdl
diff --git a/poretools.wdl b/poretools.wdl
deleted file mode 100644
index 95dce6c..0000000
--- a/poretools.wdl
+++ /dev/null
@@ -1,40 +0,0 @@
-task fastq {
- Array[File]+ files # Files should exist! Also accepts multiple directories (unlike poretools).
- String outputFile
- String? preCommand
- String? type
- String? start
- String? end
- Int? minLength
- Int? maxLength
- Boolean? highQuality
- Boolean? normalQuality
- String? group
- Boolean? gzip = true
- command {
- set -e -o pipefail
- mkdir -p $(dirname ${outputFile})
- ${preCommand}
-
- (
- # Allow for multiple directory input by looping over files
- for file in ${sep=" " files}
- do
- poretools fastq \
- ${"--type " + type} \
- ${"--start " + start } \
- ${"--end " + end } \
- ${"--min-length " + minLength } \
- ${"--max-length " + maxLength } \
- ${true="--high-quality" false="" highQuality} \
- ${true="--normal-quality" false="" normalQuality} \
- ${"--group " + group} \
- $file
- done
- ) ${true="| gzip " false="" gzip}> ${outputFile}
- }
-
- output {
- File fastq = outputFile
- }
-}
\ No newline at end of file
--
GitLab