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Commit 801f813a authored by Pappas's avatar Pappas
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Remove capturing log as output

parent cd7e49ee
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1 merge request!12Adding flash task for combining overlapping reads
......@@ -4,7 +4,6 @@ task flash {
File inputR2
String outdirPath
String? outPrefix = "flash"
String? logPath = outdirPath + "/" + outPrefix + ".log"
Int? minOverlap
Int? maxOverlap
Boolean? compress = true
......@@ -22,7 +21,7 @@ task flash {
${true="--compress " false="" defined(compress)} \
${"--min-overlap=" + minOverlap} \
${"--max-overlap=" + maxOverlap} \
${inputR1} ${inputR2} 2>&1 | tee ${logPath}
${inputR1} ${inputR2}
}
output {
......@@ -31,7 +30,6 @@ task flash {
File notCombined2 = outdirPath + "/" + outPrefix + ".notCombined_2.fastq.gz"
File hist = outdirPath + "/" + outPrefix + ".hist"
File histogram = outdirPath + "/" + outPrefix + ".histogram"
String log = select_first([logPath])
}
runtime {
......
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