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  1. task diffBed {
  2. File filtered_bed
  3. File voted_bed
  4. File diffBed_directory
  5. String sample_name
  6. String docker
  7. String cluster_config
  8. String disk_size
  9. command <<<
  10. /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${filtered_bed} -files ${diffBed_directory}/centro_pericentro_region.bed ${diffBed_directory}/btu356_LCR-hs38.bed ${diffBed_directory}/Homopolyer.hg38.bed ${diffBed_directory}/D5.DEL ${diffBed_directory}/D5.DUP ${diffBed_directory}/D5.INV ${diffBed_directory}/sv.del.break.point.500.bed ${diffBed_directory}/sv.dup.break.point.500.bed ${diffBed_directory}/sv.ins.break.point.500.bed ${diffBed_directory}/sv.inv.break.point.1000.bed ${diffBed_directory}/sv.tra.break.point.5000.bed > ${sample_name}.diffBed.filtered.txt
  11. /opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${voted_bed} -files ${diffBed_directory}/centro_pericentro_region.bed ${diffBed_directory}/btu356_LCR-hs38.bed ${diffBed_directory}/Homopolyer.hg38.bed ${diffBed_directory}/D5.DEL ${diffBed_directory}/D5.DUP ${diffBed_directory}/D5.INV ${diffBed_directory}/sv.del.break.point.500.bed ${diffBed_directory}/sv.dup.break.point.500.bed ${diffBed_directory}/sv.ins.break.point.500.bed ${diffBed_directory}/sv.inv.break.point.1000.bed ${diffBed_directory}/sv.tra.break.point.5000.bed > ${sample_name}.diffBed.voted.txt
  12. >>>
  13. runtime {
  14. docker:docker
  15. cluster: cluster_config
  16. systemDisk: "cloud_ssd 40"
  17. dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  18. }
  19. output {
  20. File filtered_diffBed = "${sample_name}.diffBed.filtered.txt"
  21. File voted_diffBed = "${sample_name}.diffBed.voted.txt"
  22. }
  23. }