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Commit 8c40b9e5 authored by Ruben Vorderman's avatar Ruben Vorderman
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seqtk to 1.0

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1 merge request!34Move all files to version 1.0
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seqtk.wdl
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version 1.0
task sample { task sample {
File sequenceFile input {
String? outFilePath = "subsampledReads.fq.gz" File sequenceFile
String? preCommand String? outFilePath = "subsampledReads.fq.gz"
Int? seed String? preCommand
Boolean? twoPassMode Int? seed
Float? fraction Boolean? twoPassMode
Int? number Float? fraction
Boolean? zip = true Int? number
Boolean? zip = true
}
command { command {
set -e -o pipefail set -e -o pipefail
${'mkdir -p $(dirname ' + outFilePath + ')'} ~{'mkdir -p $(dirname ' + outFilePath + ')'}
${preCommand} ~{preCommand}
seqtk sample \ seqtk sample \
${"-s " + seed} \ ~{"-s " + seed} \
${true="-2 " false="" twoPassMode} \ ~{true="-2 " false="" twoPassMode} \
${sequenceFile} \ ~{sequenceFile} \
${number} ${fraction} \ ~{number} ~{fraction} \
${true="| gzip" false="" zip} \ ~{true="| gzip" false="" zip} \
${"> " + outFilePath} ~{"> " + outFilePath}
} }
output { output {
File subsampledReads= select_first([outFilePath]) File subsampledReads= select_first([outFilePath])
......
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