diff --git a/biopet.wdl b/biopet.wdl index 6e5ae10aafaf9e3125999b00e1634bb728a0bb99..c87c03d6bf9adcae61b7f2ce17507a99c062d892 100644 --- a/biopet.wdl +++ b/biopet.wdl @@ -280,7 +280,7 @@ task Seqstat { String? preCommand File? toolJar File fastq - String outputFile + String outputFilePath Float? memory Float? memoryMultiplier Int mem = ceil(select_first([memory, 4.0])) @@ -292,13 +292,13 @@ task Seqstat { command { set -e -o pipefail ${preCommand} - mkdir -p ${outputFile} + mkdir -p ${outputFilePath} ${toolCommand} \ --fastq ${fastq} \ - --output ${outputFile} + --output ${outputFilePath} } output { - File seqstatsJson = outputFile + File json = outputFilePath } runtime { memory: ceil(mem * select_first([memoryMultiplier, 2.0]))