diff --git a/common.wdl b/common.wdl index 4acd8bd48c0fb60a954f26a6b4b7bf654dcecc01..2ac9cb99366ab27e768c29a947bf239064193186 100644 --- a/common.wdl +++ b/common.wdl @@ -51,12 +51,13 @@ task concatenateTextFiles { Array[File] fileList String combinedFilePath Boolean? unzip=false + Boolean? zip=false command { set -e -o pipefail ${"mkdir -p $(dirname " + combinedFilePath + ")"} ${true='zcat' false= 'cat' unzip} ${sep=' ' fileList} \ - > ${combinedFilePath} + ${true="| gzip -c" false="" zip} > ${combinedFilePath} } output {