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пре 5 година
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  1. task VCFrename {
  2. File mother_vcf_gz
  3. File father_vcf_gz
  4. File twins_vcf_gz
  5. File mother_vcf_idx
  6. File father_vcf_idx
  7. File twins_vcf_idx
  8. String mother_name
  9. String father_name
  10. String family_name
  11. String docker
  12. String cluster_config
  13. String disk_size
  14. command <<<
  15. echo "MOTHER ${mother_name}" > mother_rename.txt
  16. rtg vcfannotate -i ${mother_vcf_gz} -o ${mother_name}.rename.vcf.gz --relabel=mother_rename.txt
  17. echo "FATHER ${father_name}" > father_rename.txt
  18. rtg vcfannotate -i ${father_vcf_gz} -o ${father_name}.rename.vcf.gz --relabel=father_rename.txt
  19. echo "CHILD ${family_name}" > child_rename.txt
  20. rtg vcfannotate -i ${twins_vcf_gz} -o ${family_name}.twins.rename.vcf.gz --relabel=child_rename.txt
  21. >>>
  22. runtime {
  23. docker:docker
  24. cluster: cluster_config
  25. systemDisk: "cloud_ssd 40"
  26. dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  27. }
  28. output {
  29. File rename_mother_vcf_gz = "${mother_name}.rename.vcf.gz"
  30. File rename_father_vcf_gz = "${father_name}.rename.vcf.gz"
  31. File rename_twins_vcf_gz = "${family_name}.twins.rename.vcf.gz"
  32. File rename_mother_vcf_idx = "${mother_name}.rename.vcf.gz.tbi"
  33. File rename_father_vcf_idx = "${father_name}.rename.vcf.gz.tbi"
  34. File rename_twins_vcf_idx = "${family_name}.twins.rename.vcf.gz.tbi"
  35. }
  36. }