diff --git a/biopet.wdl b/biopet.wdl index 10ba295468f5360a62e34247ec7f80516067cc38..286b2e0e9459c89c92259bd50b94aae973f0875a 100644 --- a/biopet.wdl +++ b/biopet.wdl @@ -280,25 +280,25 @@ task Seqstat { String? preCommand File? toolJar File fastq - String outputFilePath + String outputFile Float? memory Float? memoryMultiplier Int mem = ceil(select_first([memory, 4.0])) String toolCommand = if defined(toolJar) - then "java -Xmx" + mem + "G -jar " +toolJar + then "java -Xmx" + mem + "G -jar " + toolJar else "biopet-seqstat -Xmx" + mem + "G" command { set -e -o pipefail ${preCommand} - mkdir -p $(dirname ${outputFilePath}) + mkdir -p $(dirname ${outputFile}) ${toolCommand} \ --fastq ${fastq} \ - --output ${outputFilePath} + --output ${outputFile} } output { - File json = outputFilePath + File json = outputFile } runtime { memory: ceil(mem * select_first([memoryMultiplier, 2.0]))