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benchmark_calls_gvcf
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benchmark_calls_gvcf/tasks/votes.wdl

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  1. task votes {

  2. 	Array[File] family_mendelian_info

  3. 	File vcf 

  4. 	String chromo

  5. 	String docker

  6. 	String cluster_config

  7. 	String disk_size

  8. 	

  9. 	command <<<

  10. 		mkdir temp

  11. 		for i in ${sep=" " family_mendelian_info}

  12. 		do

  13. 			cp $i temp

  14. 		done

  15. 

  16. 		cat ${vcf} | grep -v '##' > vcf_info.txt

  17. 

  18. 		python /opt/voted_by_vcfinfo_mendelianinfo.py -folder ./temp -vcf vcf_info.txt

  19. 

  20. 		cp LCL5_voted.vcf LCL5.${chromo}.voted.vcf

  21. 		cp LCL6_voted.vcf LCL6.${chromo}.voted.vcf

  22. 		cp LCL7_voted.vcf LCL7.${chromo}.voted.vcf

  23. 		cp LCL8_voted.vcf LCL8.${chromo}.voted.vcf

  24. 

  25. 	>>>

  26. 

  27. 	runtime {

  28. 		docker:docker

  29. 		cluster: cluster_config

  30. 		systemDisk: "cloud_ssd 40"

  31. 		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"

  32. 	}

  33. 	output {

  34. 		File LCL5_voted_vcf = "LCL5.${chromo}.voted.vcf"

  35. 		File LCL6_voted_vcf = "LCL6.${chromo}.voted.vcf"

  36. 		File LCL7_voted_vcf = "LCL7.${chromo}.voted.vcf"

  37. 		File LCL8_voted_vcf = "LCL8.${chromo}.voted.vcf"

  38. 		File all_sample_info = "all_sample_information.txt"

  39. 	}

  40. }