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