diff --git a/biopet.wdl b/biopet.wdl index 054a16681a68883b6f0d4d6ffc8758aca78dc0f6..e13d7630e473dbf1f758430dfe1204f512996ec3 100644 --- a/biopet.wdl +++ b/biopet.wdl @@ -90,6 +90,33 @@ task FastqSplitter { } } +task FastqSync { + String? preCommand + File ref1 + File ref2 + File in1 + File in2 + String out1path + String out2path + File tool_jar + command { + set -e -o pipefail + ${preCommand} + mkdir -p $(dirname ${out1path}) $(dirname ${out2path}) + java -jar ${tool_jar} \ + --in1 ${in1} \ + --in2 ${in2} \ + --ref1 ${ref1} \ + --ref2 ${ref2} \ + --out1 ${out1path} \ + --out2 ${out2path} + } + output { + File out1 = out1path + File out2 = out2path + } +} + task SampleConfig { String? preCommand String tool_jar