From 758de0e5a9725170d52ee61093a40c1addd79e43 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 23 Jul 2018 12:59:31 +0200
Subject: [PATCH] biopet.wdl to 1.0
---
biopet.wdl | 207 +++++++++++++++++++++++++++++------------------------
1 file changed, 114 insertions(+), 93 deletions(-)
diff --git a/biopet.wdl b/biopet.wdl
index a1bf3d7..bde7390 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -1,16 +1,20 @@
+version 1.0
+
task BaseCounter {
- String? preCommand
- File? toolJar
- File bam
- File bamIndex
- File refFlat
- String outputDir
- String prefix
-
- Float? memory
- Float? memoryMultiplier
- Int mem = ceil(select_first([memory, 4.0]))
+ input {
+ String? preCommand
+ File? toolJar
+ File bam
+ File bamIndex
+ File refFlat
+ String outputDir
+ String prefix
+
+ Float? memory
+ Float? memoryMultiplier
+ }
+ Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(toolJar)
then "java -Xmx" + mem + "G -jar " +toolJar
else "biopet-basecounter -Xmx" + mem + "G"
@@ -69,20 +73,22 @@ task BaseCounter {
}
task ExtractAdaptersFastqc {
- File? toolJar
- String? preCommand
- 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
+ input {
+ File? toolJar
+ String? preCommand
+ 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]))
String toolCommand = if defined(toolJar)
@@ -117,15 +123,17 @@ task ExtractAdaptersFastqc {
}
task FastqSplitter {
- String? preCommand
- File inputFastq
- Array[String] outputPaths
- File? toolJar
+ input {
+ String? preCommand
+ File inputFastq
+ Array[String] outputPaths
+ File? toolJar
+
+ Float? memory
+ Float? memoryMultiplier
+ }
- Float? memory
- Float? memoryMultiplier
Int mem = ceil(select_first([memory, 4.0]))
-
String toolCommand = if defined(toolJar)
then "java -Xmx" + mem + "G -jar " +toolJar
else "biopet-fastqsplitter -Xmx" + mem + "G"
@@ -153,17 +161,19 @@ task FastqSplitter {
}
task FastqSync {
- String? preCommand
- File ref1
- File ref2
- File in1
- File in2
- String out1path
- String out2path
- File? toolJar
-
- Float? memory
- Float? memoryMultiplier
+ input {
+ String? preCommand
+ File ref1
+ File ref2
+ File in1
+ File in2
+ String out1path
+ String out2path
+ File? toolJar
+
+ Float? memory
+ Float? memoryMultiplier
+ }
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(toolJar)
@@ -194,18 +204,20 @@ task FastqSync {
}
task SampleConfig {
- File? toolJar
- String? preCommand
- Array[File]+ inputFiles
- String keyFilePath
- String? sample
- String? library
- String? readgroup
- String? jsonOutputPath
- String? tsvOutputPath
-
- Float? memory
- Float? memoryMultiplier
+ input {
+ File? toolJar
+ String? preCommand
+ Array[File]+ inputFiles
+ String keyFilePath
+ String? sample
+ String? library
+ String? readgroup
+ String? jsonOutputPath
+ String? tsvOutputPath
+ Float? memory
+ Float? memoryMultiplier
+ }
+
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(toolJar)
@@ -238,16 +250,18 @@ task SampleConfig {
}
task ScatterRegions {
- String? preCommand
- File refFasta
- File refDict
- String outputDirPath
- File? toolJar
- Int? scatterSize
- File? regions
-
- Float? memory
- Float? memoryMultiplier
+ input {
+ String? preCommand
+ File refFasta
+ File refDict
+ String outputDirPath
+ File? toolJar
+ Int? scatterSize
+ File? regions
+
+ Float? memory
+ Float? memoryMultiplier
+ }
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(toolJar)
@@ -275,12 +289,14 @@ task ScatterRegions {
}
task Seqstat {
- String? preCommand
- File? toolJar
- File fastq
- String outputFile
- Float? memory
- Float? memoryMultiplier
+ input {
+ String? preCommand
+ File? toolJar
+ File fastq
+ String outputFile
+ Float? memory
+ Float? memoryMultiplier
+ }
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(toolJar)
@@ -306,14 +322,15 @@ task Seqstat {
}
task ValidateAnnotation {
- String? preCommand
- File? toolJar
- File? refRefflat
- File? gtfFile
- File refFasta
-
- Float? memory
- Float? memoryMultiplier
+ input {
+ String? preCommand
+ File? toolJar
+ File? refRefflat
+ File? gtfFile
+ File refFasta
+ Float? memory
+ Float? memoryMultiplier
+ }
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(toolJar)
@@ -339,13 +356,15 @@ task ValidateAnnotation {
}
task ValidateFastq {
- String? preCommand
- File? toolJar
- File fastq1
- File? fastq2
-
- Float? memory
- Float? memoryMultiplier
+ input {
+ String? preCommand
+ File? toolJar
+ File fastq1
+ File? fastq2
+
+ Float? memory
+ Float? memoryMultiplier
+ }
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(toolJar)
@@ -370,13 +389,15 @@ task ValidateFastq {
}
task ValidateVcf {
- String? preCommand
- File? toolJar
- File vcfFile
- File refFasta
-
- Float? memory
- Float? memoryMultiplier
+ input {
+ String? preCommand
+ File? toolJar
+ File vcfFile
+ File refFasta
+
+ Float? memory
+ Float? memoryMultiplier
+ }
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(toolJar)
--
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