diff --git a/delly.wdl b/delly.wdl new file mode 100644 index 0000000000000000000000000000000000000000..2fc63cda80a8ec9d8310abfe1cd6d29f02f2f104 --- /dev/null +++ b/delly.wdl @@ -0,0 +1,30 @@ +version 1.0 + +import "common.wdl" + +task CallSV { + input { + IndexedBamFile bamFile + Reference reference + String outputPath + } + + + command <<< + set -e + mkdir -p $(dirname ~{outputPath}) + delly call \ + -o ~{outputPath} \ + -g ~{reference.fasta} \ + ~{bamFile.file} + >>> + + output { + File dellyBcf = "~{outputPath}" + } + + runtime { + docker: "quay.io/biocontainers/delly:0.8.1--h4037b6b_1" + } + +}