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bcf2vcf.wdl 1.1KB

5 år sedan
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  1. task bcf2vcf {
  2. File ins_bcf
  3. File ins_bcf_index
  4. File del_bcf
  5. File del_bcf_index
  6. File dup_bcf
  7. File dup_bcf_index
  8. File inv_bcf
  9. File inv_bcf_index
  10. File bnd_bcf
  11. File bnd_bcf_index
  12. String sample_name
  13. String docker
  14. String disk_size
  15. String cluster_config
  16. command <<<
  17. set -o pipefail
  18. set -e
  19. /opt/hall-lab/bcftools-1.9/bin/bcftools view ${ins_bcf} > ${sample_name}.ins.vcf
  20. /opt/hall-lab/bcftools-1.9/bin/bcftools view ${del_bcf} > ${sample_name}.del.vcf
  21. /opt/hall-lab/bcftools-1.9/bin/bcftools view ${dup_bcf} > ${sample_name}.dup.vcf
  22. /opt/hall-lab/bcftools-1.9/bin/bcftools view ${inv_bcf} > ${sample_name}.inv.vcf
  23. /opt/hall-lab/bcftools-1.9/bin/bcftools view ${bnd_bcf} > ${sample_name}.bnd.vcf
  24. >>>
  25. runtime {
  26. docker:docker
  27. cluster:cluster_config
  28. systemDisk: "cloud_ssd 40"
  29. dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  30. }
  31. output {
  32. File ins_vcf = "${sample_name}.ins.vcf"
  33. File del_vcf = "${sample_name}.del.vcf"
  34. File dup_vcf = "${sample_name}.dup.vcf"
  35. File inv_vcf = "${sample_name}.inv.vcf"
  36. File bnd_vcf = "${sample_name}.bnd.vcf"
  37. }
  38. }