diff --git a/bcftools.wdl b/bcftools.wdl new file mode 100644 index 0000000000000000000000000000000000000000..de7730bbd554cbe05079d93756aa424152d9610b --- /dev/null +++ b/bcftools.wdl @@ -0,0 +1,22 @@ +version 1.0 + +task Bcf2Vcf { + input { + File bcf + String outputPath + } + + command <<< + set -e + mkdir -p $(dirname ~{outputPath}) + bcftools view ~{bcf} -O v -o ~{outputPath} + >>> + + output { + File OutputVcf = "~{outputPath}" + } + + runtime { + docker: "quay.io/biocontainers/bcftools:1.9--ha228f0b_3" + } +}