diff --git a/flash.wdl b/flash.wdl index 673da3d6b415a70f3787cc0b4e5e427edb208736..3fbe0ed3c2f631a946497ebf001ca40ffe26b455 100644 --- a/flash.wdl +++ b/flash.wdl @@ -16,9 +16,9 @@ task flash { String? preCommand File inputR1 File inputR2 - String outDirPath + String outdirPath String? outPrefix = "flash" - String? logPath = outDirPath + "/" + outPrefix + ".log" + String? logPath = outdirPath + "/" + outPrefix + ".log" Int? minOverlap Int? maxOverlap Boolean? compress = true @@ -27,11 +27,11 @@ task flash { command { set -e -o pipefail - mkdir -p ${outDirPath} + mkdir -p ${outdirPath} ${preCommand} flash \ ${"--threads=" + threads} \ - ${"--output-directory=" + outDirPath} \ + ${"--output-directory=" + outdirPath} \ ${"--output-prefix=" + outPrefix} \ ${true="--compress " false="" defined(compress)} \ ${"--min-overlap=" + minOverlap} \ @@ -40,11 +40,11 @@ task flash { } output { - File extendedFrags = outDirPath + "/" + outPrefix + ".extendedFrags.fastq.gz" - File notCombined1 = outDirPath + "/" + outPrefix + ".notCombined_1.fastq.gz" - File notCombined2 = outDirPath + "/" + outPrefix + ".notCombined_2.fastq.gz" - File hist = outDirPath + "/" + outPrefix + ".hist" - File histogram = outDirPath + "/" + outPrefix + ".histogram" + File extendedFrags = outdirPath + "/" + outPrefix + ".extendedFrags.fastq.gz" + File notCombined1 = outdirPath + "/" + outPrefix + ".notCombined_1.fastq.gz" + File notCombined2 = outdirPath + "/" + outPrefix + ".notCombined_2.fastq.gz" + File hist = outdirPath + "/" + outPrefix + ".hist" + File histogram = outdirPath + "/" + outPrefix + ".histogram" String log = select_first([logPath]) }