diff --git a/seqtk.wdl b/seqtk.wdl new file mode 100644 index 0000000000000000000000000000000000000000..935669ce700f0f78b33092875919bcd33a825764 --- /dev/null +++ b/seqtk.wdl @@ -0,0 +1,25 @@ +task sample { + File sequenceFile + File? outFilePath = "subsampledReads" + String? preCommand + Int? seed + Boolean? twoPassMode + Float? fraction + Int? number + Boolean? zip + + command { + set -e -o pipefail + ${preCommand} + seqtk sample \ + ${"-s " + seed} \ + ${true="-2 " false="" twoPassMode} \ + ${sequenceFile} \ + ${number} ${fraction} \ + ${true="| gzip" false="" zip} \ + ${"> " + outFilePath} + } + output { + File subsampledReads=select_first([outFilePath]) + } +} \ No newline at end of file