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Commit 9249f3e2 authored by Ruben Vorderman's avatar Ruben Vorderman
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flash to 1.0

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1 merge request!34Move all files to version 1.0
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flash.wdl
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version 1.0
task flash { task flash {
String? preCommand input {
File inputR1 String? preCommand
File inputR2 File inputR1
String outdirPath File inputR2
String? outPrefix = "flash" String outdirPath
Int? minOverlap String? outPrefix = "flash"
Int? maxOverlap Int? minOverlap
Boolean? compress = true Int? maxOverlap
Int? threads Boolean? compress = true
Int? memory Int? threads
Int? memory
}
command { command {
set -e -o pipefail set -e -o pipefail
mkdir -p ${outdirPath} mkdir -p ~{outdirPath}
${preCommand} ~{preCommand}
flash \ flash \
${"--threads=" + threads} \ ~{"--threads=" + threads} \
${"--output-directory=" + outdirPath} \ ~{"--output-directory=" + outdirPath} \
${"--output-prefix=" + outPrefix} \ ~{"--output-prefix=" + outPrefix} \
${true="--compress " false="" defined(compress)} \ ~{true="--compress " false="" defined(compress)} \
${"--min-overlap=" + minOverlap} \ ~{"--min-overlap=" + minOverlap} \
${"--max-overlap=" + maxOverlap} \ ~{"--max-overlap=" + maxOverlap} \
${inputR1} ${inputR2} ~{inputR1} ~{inputR2}
} }
output { output {
......
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