diff --git a/biopet.wdl b/biopet.wdl index 286b2e0e9459c89c92259bd50b94aae973f0875a..91030693ec8b0b074926f020a170482643a5ee6a 100644 --- a/biopet.wdl +++ b/biopet.wdl @@ -305,3 +305,29 @@ task Seqstat { } } +task ValidateFastq { + String? preCommand + File? toolJar + File fastq1 + File? fastq2 + + Float? memory + Float? memoryMultiplier + Int mem = ceil(select_first([memory, 4.0])) + + String toolCommand = if defined(toolJar) + then "java -Xmx" + mem + "G -jar " + toolJar + else "biopet-validatefastq -Xmx" + mem + "G" + + command { + set -e -o pipefail + ${preCommand} + biopet-validatefastq \ + --fastq1 ${fastq1} \ + ${"--fastq2 " + fastq2} + } + output { + File stderr = stderr() + } +} +