diff --git a/flash.wdl b/flash.wdl index 90c522e0436b16f374c24d439e0c1f3e9cebbd1d..c081d49cdd3841e91991b0c90ac894d61d965e40 100644 --- a/flash.wdl +++ b/flash.wdl @@ -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 {