diff --git a/stringtie.wdl b/stringtie.wdl index e8c74d71e671bfebe9ad5e641311f79e809d2b58..cba707620243553bd36a1c5cde1980ac7c2666d8 100644 --- a/stringtie.wdl +++ b/stringtie.wdl @@ -3,7 +3,7 @@ task Stringtie { File alignedReads File? referenceGFF Int? threads - String assembledTranscripts + String assembledTranscriptsFile command { set -e -o pipefail @@ -12,11 +12,11 @@ task Stringtie { ${"-p " + threads} \ ${"-G " + referenceGFF} \ ${alignedReads} \ - > ${assembledTranscripts} + > ${assembledTranscriptsFile} } output { - File assembledTranscripts = assembledTranscripts + File assembledTranscripts = assembledTranscriptsFile } runtime {