diff --git a/cutadapt.wdl b/cutadapt.wdl index e89531b1decdf1e35ed3a34529b42e92ee409b27..0df1ced44f253b904586c7a89b7dc61436181551 100644 --- a/cutadapt.wdl +++ b/cutadapt.wdl @@ -61,12 +61,12 @@ task Cutadapt { String? reportPath } - String read2outputarg = if (defined(read2output)) then "mkdir -p $(dirname " + read2output + ")" else "" + String read2outputArg = if (defined(read2output)) then "mkdir -p $(dirname " + read2output + ")" else "" command { set -e -o pipefail ~{"mkdir -p $(dirname " + read1output + ")"} - ~{read2outputarg} + ~{read2outputArg} ~{"mkdir -p $(dirname " + reportPath + ")"} ~{preCommand} cutadapt \