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Commit ebc94bdb authored by Ruben Vorderman's avatar Ruben Vorderman
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stringtie to 1.0

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1 merge request!34Move all files to version 1.0
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stringtie.wdl
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version 1.0
task Stringtie { task Stringtie {
String? preCommand input {
File alignedReads String? preCommand
File? referenceGtf File alignedReads
Int? threads File? referenceGtf
String assembledTranscriptsFile Int? threads
Boolean? firstStranded String assembledTranscriptsFile
Boolean? secondStranded Boolean? firstStranded
String? geneAbundanceFile Boolean? secondStranded
String? geneAbundanceFile
}
command { command {
set -e -o pipefail set -e -o pipefail
mkdir -p $(dirname ${assembledTranscriptsFile}) mkdir -p $(dirname ~{assembledTranscriptsFile})
${preCommand} ~{preCommand}
stringtie \ stringtie \
${"-p " + threads} \ ~{"-p " + threads} \
${"-G " + referenceGtf} \ ~{"-G " + referenceGtf} \
${true="--rf" false="" firstStranded} \ ~{true="--rf" false="" firstStranded} \
${true="fr" false="" secondStranded} \ ~{true="fr" false="" secondStranded} \
-o ${assembledTranscriptsFile} \ -o ~{assembledTranscriptsFile} \
${"-A " + geneAbundanceFile} \ ~{"-A " + geneAbundanceFile} \
${alignedReads} \ ~{alignedReads} \
} }
......
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