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Commit 2b903b2b authored by Ruben Vorderman's avatar Ruben Vorderman
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style fixes

parent 91da0d8f
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1 merge request!34Move all files to version 1.0
......@@ -120,7 +120,7 @@ task Classify {
}
task Download {
input {
input {
String libraryPath
Array[String]? domain
String? executable = "centrifuge-download"
......
......@@ -24,27 +24,27 @@ task fastqc {
# This regex chops of the extension and replaces it with _fastqc for the reportdir.
# Just as fastqc does it.
String reportDir = outdirPath + "/" + sub(basename(name), "\\.[^\\.]*$", "_fastqc")
command {
set -e -o pipefail
~{preCommand}
mkdir -p ~{outdirPath}
fastqc \
~{"--outdir " + outdirPath} \
~{true="--casava" false="" casava} \
~{true="--nano" false="" nano} \
~{true="--nofilter" false="" noFilter} \
~{true="--extract" false="" extract} \
~{true="--nogroup" false="" nogroup} \
~{"--min_length " + minLength } \
~{"--format " + format} \
~{"--threads " + threads} \
~{"--contaminants " + contaminants} \
~{"--adapters " + adapters} \
~{"--limits " + limits} \
~{"--kmers " + kmers} \
~{"--dir " + dir} \
~{seqFile}
command {
set -e -o pipefail
~{preCommand}
mkdir -p ~{outdirPath}
fastqc \
~{"--outdir " + outdirPath} \
~{true="--casava" false="" casava} \
~{true="--nano" false="" nano} \
~{true="--nofilter" false="" noFilter} \
~{true="--extract" false="" extract} \
~{true="--nogroup" false="" nogroup} \
~{"--min_length " + minLength } \
~{"--format " + format} \
~{"--threads " + threads} \
~{"--contaminants " + contaminants} \
~{"--adapters " + adapters} \
~{"--limits " + limits} \
~{"--kmers " + kmers} \
~{"--dir " + dir} \
~{seqFile}
}
output {
......
......@@ -141,18 +141,18 @@ task view {
}
command {
set -e -o pipefail
~{preCommand}
samtools view \
~{"-T " + referenceFasta} \
~{"-o " + outputFileName} \
~{true="-b " false="" outputBam} \
~{true="-u " false="" uncompressedBamOutput} \
~{"-f " + includeFilter} \
~{"-F " + excludeFilter} \
~{"-G " + excludeSpecificFilter} \
~{"--threads " + threads - 1} \
~{inFile}
set -e -o pipefail
~{preCommand}
samtools view \
~{"-T " + referenceFasta} \
~{"-o " + outputFileName} \
~{true="-b " false="" outputBam} \
~{true="-u " false="" uncompressedBamOutput} \
~{"-f " + includeFilter} \
~{"-F " + excludeFilter} \
~{"-G " + excludeSpecificFilter} \
~{"--threads " + threads - 1} \
~{inFile}
}
output {
......
......@@ -23,8 +23,7 @@ task Stringtie {
~{true="fr" false="" secondStranded} \
-o ~{assembledTranscriptsFile} \
~{"-A " + geneAbundanceFile} \
~{alignedReads} \
~{alignedReads}
}
output {
......
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