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Commit f38b3de1 authored by Pappas's avatar Pappas
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outDirPath to outdirPath for compatibility

parent d922d7b9
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1 merge request!12Adding flash task for combining overlapping reads
...@@ -16,9 +16,9 @@ task flash { ...@@ -16,9 +16,9 @@ task flash {
String? preCommand String? preCommand
File inputR1 File inputR1
File inputR2 File inputR2
String outDirPath String outdirPath
String? outPrefix = "flash" String? outPrefix = "flash"
String? logPath = outDirPath + "/" + outPrefix + ".log" String? logPath = outdirPath + "/" + outPrefix + ".log"
Int? minOverlap Int? minOverlap
Int? maxOverlap Int? maxOverlap
Boolean? compress = true Boolean? compress = true
...@@ -27,11 +27,11 @@ task flash { ...@@ -27,11 +27,11 @@ task flash {
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} \
...@@ -40,11 +40,11 @@ task flash { ...@@ -40,11 +40,11 @@ task flash {
} }
output { output {
File extendedFrags = outDirPath + "/" + outPrefix + ".extendedFrags.fastq.gz" File extendedFrags = outdirPath + "/" + outPrefix + ".extendedFrags.fastq.gz"
File notCombined1 = outDirPath + "/" + outPrefix + ".notCombined_1.fastq.gz" File notCombined1 = outdirPath + "/" + outPrefix + ".notCombined_1.fastq.gz"
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]) String log = select_first([logPath])
} }
......
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