From dce75b054af8cd12e7badf64faa67ef6107c0879 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 29 Jan 2018 15:37:56 +0100
Subject: [PATCH] getConfiguration task
---
fastqc.wdl | 16 ++++++++++++++++
1 file changed, 16 insertions(+)
diff --git a/fastqc.wdl b/fastqc.wdl
index e245a0a..630ee15 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -94,4 +94,20 @@ task extractAdapters {
Array[String] adapterList = read_lines(select_first([adapterOutputFilePath]))
Array[String] contamsList = read_lines(select_first([contamsOutputFilePath]))
}
+}
+
+task getConfiguration {
+ String? preCommand
+ String? fastqcDirFile = "fastqcDir.txt"
+ command {
+ set -e -o pipefail
+ ${preCommand}
+ echo $(dirname $(readlink -f $(which fastqc))) > ${fastqcDirFile}
+ }
+ output {
+ String fastqcDir = read_string(fastqcDirFile)
+ File adapterList = fastqcDir + "/Configuration/adapter_list.txt"
+ File contaminantList = fastqcDir + "/Configuration/contaminant_list.txt"
+ File limits = fastqcDir + "/Configuration/limits.txt"
+ }
}
\ No newline at end of file
--
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