From 3270612609d12a4bab5909208b8d1875d4c1b468 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 28 May 2018 13:15:22 +0200
Subject: [PATCH] move extractadaptersfastqc to biopet
---
biopet.wdl | 43 +++++++++++++++++++++++++++++++++++++++++++
fastqc.wdl | 42 ------------------------------------------
2 files changed, 43 insertions(+), 42 deletions(-)
diff --git a/biopet.wdl b/biopet.wdl
index 7d0d0a5..8d91955 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -65,6 +65,49 @@ task BaseCounter {
}
}
+task extractAdapters {
+ File extractAdaptersFastqcJar
+ File inputFile
+ String outputDir
+ String? adapterOutputFilePath = outputDir + "/adapter.list"
+ String? contamsOutputFilePath = outputDir + "/contaminations.list"
+ Boolean? skipContams
+ File? knownContamFile
+ File? knownAdapterFile
+ Float? adapterCutoff
+ Boolean? outputAsFasta
+
+ Float? memory
+ Float? memoryMultiplier
+
+ Int mem = ceil(select_first([memory, 4.0]))
+ command {
+ set -e
+ mkdir -p ${outputDir}
+ java -Xmx${mem}G -jar ${extractAdaptersFastqcJar} \
+ --inputFile ${inputFile} \
+ ${"--adapterOutputFile " + adapterOutputFilePath } \
+ ${"--contamsOutputFile " + contamsOutputFilePath } \
+ ${"--knownContamFile " + knownContamFile} \
+ ${"--knownAdapterFile " + knownAdapterFile} \
+ ${"--adapterCutoff " + adapterCutoff} \
+ ${true="--skipContams" false="" skipContams} \
+ ${true="--outputAsFasta" false="" outputAsFasta}
+ }
+
+ output {
+ File adapterOutputFile = select_first([adapterOutputFilePath])
+ File contamsOutputFile = select_first([contamsOutputFilePath])
+ Array[String] adapterList = read_lines(select_first([adapterOutputFilePath]))
+ Array[String] contamsList = read_lines(select_first([contamsOutputFilePath]))
+ }
+
+ runtime {
+ memory: ceil(mem * select_first([memoryMultiplier, 2.5]))
+ }
+}
+
+
task FastqSplitter {
String? preCommand
File inputFastq
diff --git a/fastqc.wdl b/fastqc.wdl
index f0fd2fe..d9135f7 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -55,48 +55,6 @@ task fastqc {
}
}
-task extractAdapters {
- File extractAdaptersFastqcJar
- File inputFile
- String outputDir
- String? adapterOutputFilePath = outputDir + "/adapter.list"
- String? contamsOutputFilePath = outputDir + "/contaminations.list"
- Boolean? skipContams
- File? knownContamFile
- File? knownAdapterFile
- Float? adapterCutoff
- Boolean? outputAsFasta
-
- Float? memory
- Float? memoryMultiplier
-
- Int mem = ceil(select_first([memory, 4.0]))
- command {
- set -e
- mkdir -p ${outputDir}
- java -Xmx${mem}G -jar ${extractAdaptersFastqcJar} \
- --inputFile ${inputFile} \
- ${"--adapterOutputFile " + adapterOutputFilePath } \
- ${"--contamsOutputFile " + contamsOutputFilePath } \
- ${"--knownContamFile " + knownContamFile} \
- ${"--knownAdapterFile " + knownAdapterFile} \
- ${"--adapterCutoff " + adapterCutoff} \
- ${true="--skipContams" false="" skipContams} \
- ${true="--outputAsFasta" false="" outputAsFasta}
- }
-
- output {
- File adapterOutputFile = select_first([adapterOutputFilePath])
- File contamsOutputFile = select_first([contamsOutputFilePath])
- Array[String] adapterList = read_lines(select_first([adapterOutputFilePath]))
- Array[String] contamsList = read_lines(select_first([contamsOutputFilePath]))
- }
-
- runtime {
- memory: ceil(mem * select_first([memoryMultiplier, 2.5]))
- }
-}
-
task getConfiguration {
String? preCommand
String? fastqcDirFile = "fastqcDir.txt"
--
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