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Commit 39cbad54 authored by Ruben Vorderman's avatar Ruben Vorderman
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fastqc to 1.0

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1 merge request!34Move all files to version 1.0
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fastqc.wdl
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version 1.0
task fastqc { task fastqc {
File seqFile input {
String outdirPath File seqFile
String? preCommand String outdirPath
Boolean? casava String? preCommand
Boolean? nano Boolean? casava
Boolean? noFilter Boolean? nano
Boolean? extract = true Boolean? noFilter
Boolean? nogroup Boolean? extract = true
Int? minLength Boolean? nogroup
String? format Int? minLength
Int? threads = 1 String? format
File? contaminants Int? threads = 1
File? adapters File? contaminants
File? limits File? adapters
Int? kmers File? limits
String? dir Int? kmers
String? dir
}
# Chops of the .gz extension if present. # Chops of the .gz extension if present.
String name = sub(seqFile, "\\.gz$","") String name = sub(seqFile, "\\.gz$","")
# This regex chops of the extension and replaces it with _fastqc for the reportdir. # This regex chops of the extension and replaces it with _fastqc for the reportdir.
...@@ -22,24 +26,24 @@ task fastqc { ...@@ -22,24 +26,24 @@ task fastqc {
String reportDir = outdirPath + "/" + sub(basename(name), "\\.[^\\.]*$", "_fastqc") String reportDir = outdirPath + "/" + sub(basename(name), "\\.[^\\.]*$", "_fastqc")
command { command {
set -e -o pipefail set -e -o pipefail
${preCommand} ~{preCommand}
mkdir -p ${outdirPath} mkdir -p ~{outdirPath}
fastqc \ fastqc \
${"--outdir " + outdirPath} \ ~{"--outdir " + outdirPath} \
${true="--casava" false="" casava} \ ~{true="--casava" false="" casava} \
${true="--nano" false="" nano} \ ~{true="--nano" false="" nano} \
${true="--nofilter" false="" noFilter} \ ~{true="--nofilter" false="" noFilter} \
${true="--extract" false="" extract} \ ~{true="--extract" false="" extract} \
${true="--nogroup" false="" nogroup} \ ~{true="--nogroup" false="" nogroup} \
${"--min_length " + minLength } \ ~{"--min_length " + minLength } \
${"--format " + format} \ ~{"--format " + format} \
${"--threads " + threads} \ ~{"--threads " + threads} \
${"--contaminants " + contaminants} \ ~{"--contaminants " + contaminants} \
${"--adapters " + adapters} \ ~{"--adapters " + adapters} \
${"--limits " + limits} \ ~{"--limits " + limits} \
${"--kmers " + kmers} \ ~{"--kmers " + kmers} \
${"--dir " + dir} \ ~{"--dir " + dir} \
${seqFile} ~{seqFile}
} }
...@@ -56,13 +60,14 @@ task fastqc { ...@@ -56,13 +60,14 @@ task fastqc {
} }
task getConfiguration { task getConfiguration {
String? preCommand input {
String? fastqcDirFile = "fastqcDir.txt" String? preCommand
String? fastqcDirFile = "fastqcDir.txt"
}
command { command {
set -e -o pipefail set -e -o pipefail
${preCommand} ~{preCommand}
echo $(dirname $(readlink -f $(which fastqc))) > ${fastqcDirFile} echo $(dirname $(readlink -f $(which fastqc))) > ~{fastqcDirFile}
} }
output { output {
......
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