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  1. task bed_annotation {
  2. File merged_vcf
  3. File merged_vcf_idx
  4. File repeat_bed
  5. String sample
  6. String docker
  7. String cluster_config
  8. String disk_size
  9. command <<<
  10. rtg vcfannotate --bed-info=${repeat_bed} -i ${merged_vcf} -o ${sample}.normed.repeatAnno.vcf.gz
  11. >>>
  12. runtime {
  13. docker:docker
  14. cluster: cluster_config
  15. systemDisk: "cloud_ssd 40"
  16. dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  17. }
  18. output {
  19. File repeat_annotated_vcf = "${sample}.normed.repeatAnno.vcf.gz"
  20. }
  21. }