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sister.wdl 918B

5 years ago
5 years ago
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  1. task sister {
  2. File LCL5_vcf
  3. File LCL6_vcf
  4. File ref_dir
  5. String fasta
  6. String family_name
  7. String docker
  8. String cluster_config
  9. String disk_size
  10. command <<<
  11. export LD_LIBRARY_PATH=/opt/htslib-1.9
  12. mkdir sister
  13. vbt varcomp -called ${LCL5_vcf} -base ${LCL6_vcf} -ref ${ref_dir}/${fasta} -outDir sister -filter none
  14. mv sister/TPBase.vcf ${family_name}.sister.consistent.vcf
  15. mv sister/FP.vcf ${family_name}.LCL5.uniq.vcf
  16. mv sister/FN.vcf ${family_name}.LCL6.uniq.vcf
  17. mv sister/log.txt ${family_name}.sister.vbt.log.txt
  18. >>>
  19. runtime {
  20. docker:docker
  21. cluster: cluster_config
  22. systemDisk: "cloud_ssd 40"
  23. dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  24. }
  25. output {
  26. File sister_consistent_vcf = "${family_name}.sister.consistent.vcf"
  27. File LCL5_uniq = "${family_name}.LCL5.uniq.vcf"
  28. File LCL6_uniq = "${family_name}.LCL6.uniq.vcf"
  29. File log = "${family_name}.sister.vbt.log.txt"
  30. }
  31. }