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Commit b31f4001 authored by Ruben Vorderman's avatar Ruben Vorderman
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add seqtk sample task

parent 06ef73d9
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2 merge requests!9Changes for virus assembly pipeline,!10Extra tasks required for assembly.
task sample {
File sequenceFile
File? outFilePath = "subsampledReads"
String? preCommand
Int? seed
Boolean? twoPassMode
Float? fraction
Int? number
Boolean? zip
command {
set -e -o pipefail
${preCommand}
seqtk sample \
${"-s " + seed} \
${true="-2 " false="" twoPassMode} \
${sequenceFile} \
${number} ${fraction} \
${true="| gzip" false="" zip} \
${"> " + outFilePath}
}
output {
File subsampledReads=select_first([outFilePath])
}
}
\ No newline at end of file
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