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SV_MIE/tasks/bedAnnotation.wdl

bedAnnotation.wdl 28KB
Исходник Normal View История

improve
5 лет назад
1500bp
4 лет назад
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improve
5 лет назад
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1500bp
4 лет назад
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​
​
​
​
​
​
​
improve
5 лет назад
​
​
​
​
​
​
​
​
​
1500bp
4 лет назад
​
​
​
​
​
​
​
​
​
improve
5 лет назад
​
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  1. task bedAnnotation {

  2. 	File filtered_bed

  3. 	File voted_bed

  4. 	File breakpoint_directory

  5. 	String sample_name

  6. 	String docker

  7. 	String cluster_config

  8. 	String disk_size

  9. 	

  10. 	command <<<

  11. 

  12. # filtered

  13. # BND

  14. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${filtered_bed} -files ${breakpoint_directory}/D5.BND.1500.left.bed ${breakpoint_directory}/D5.BND.1450.left.bed ${breakpoint_directory}/D5.BND.1400.left.bed ${breakpoint_directory}/D5.BND.1350.left.bed ${breakpoint_directory}/D5.BND.1300.left.bed ${breakpoint_directory}/D5.BND.1250.left.bed ${breakpoint_directory}/D5.BND.1200.left.bed ${breakpoint_directory}/D5.BND.1150.left.bed ${breakpoint_directory}/D5.BND.1100.left.bed ${breakpoint_directory}/D5.BND.1050.left.bed ${breakpoint_directory}/D5.BND.1000.left.bed ${breakpoint_directory}/D5.BND.950.left.bed ${breakpoint_directory}/D5.BND.900.left.bed ${breakpoint_directory}/D5.BND.850.left.bed ${breakpoint_directory}/D5.BND.800.left.bed ${breakpoint_directory}/D5.BND.750.left.bed ${breakpoint_directory}/D5.BND.700.left.bed ${breakpoint_directory}/D5.BND.650.left.bed ${breakpoint_directory}/D5.BND.600.left.bed ${breakpoint_directory}/D5.BND.550.left.bed ${breakpoint_directory}/D5.BND.500.left.bed ${breakpoint_directory}/D5.BND.450.left.bed ${breakpoint_directory}/D5.BND.400.left.bed ${breakpoint_directory}/D5.BND.350.left.bed ${breakpoint_directory}/D5.BND.300.left.bed ${breakpoint_directory}/D5.BND.250.left.bed ${breakpoint_directory}/D5.BND.200.left.bed ${breakpoint_directory}/D5.BND.150.left.bed ${breakpoint_directory}/D5.BND.100.left.bed ${breakpoint_directory}/D5.BND.50.left.bed ${breakpoint_directory}/D5.BND.50.right.bed ${breakpoint_directory}/D5.BND.100.right.bed ${breakpoint_directory}/D5.BND.150.right.bed ${breakpoint_directory}/D5.BND.200.right.bed ${breakpoint_directory}/D5.BND.250.right.bed ${breakpoint_directory}/D5.BND.300.right.bed ${breakpoint_directory}/D5.BND.350.right.bed ${breakpoint_directory}/D5.BND.400.right.bed ${breakpoint_directory}/D5.BND.450.right.bed ${breakpoint_directory}/D5.BND.500.right.bed ${breakpoint_directory}/D5.BND.550.right.bed ${breakpoint_directory}/D5.BND.600.right.bed ${breakpoint_directory}/D5.BND.650.right.bed ${breakpoint_directory}/D5.BND.700.right.bed ${breakpoint_directory}/D5.BND.750.right.bed ${breakpoint_directory}/D5.BND.800.right.bed ${breakpoint_directory}/D5.BND.850.right.bed ${breakpoint_directory}/D5.BND.900.right.bed ${breakpoint_directory}/D5.BND.950.right.bed ${breakpoint_directory}/D5.BND.1000.right.bed ${breakpoint_directory}/D5.BND.1050.right.bed ${breakpoint_directory}/D5.BND.1100.right.bed ${breakpoint_directory}/D5.BND.1150.right.bed ${breakpoint_directory}/D5.BND.1200.right.bed ${breakpoint_directory}/D5.BND.1250.right.bed ${breakpoint_directory}/D5.BND.1300.right.bed ${breakpoint_directory}/D5.BND.1350.right.bed ${breakpoint_directory}/D5.BND.1400.right.bed ${breakpoint_directory}/D5.BND.1450.right.bed ${breakpoint_directory}/D5.BND.1500.right.bed > ${sample_name}.BND.filtered.txt

  15. 

  16. # DEL

  17. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${filtered_bed} -files ${breakpoint_directory}/D5.DEL.1500.left.bed ${breakpoint_directory}/D5.DEL.1450.left.bed ${breakpoint_directory}/D5.DEL.1400.left.bed ${breakpoint_directory}/D5.DEL.1350.left.bed ${breakpoint_directory}/D5.DEL.1300.left.bed ${breakpoint_directory}/D5.DEL.1250.left.bed ${breakpoint_directory}/D5.DEL.1200.left.bed ${breakpoint_directory}/D5.DEL.1150.left.bed ${breakpoint_directory}/D5.DEL.1100.left.bed ${breakpoint_directory}/D5.DEL.1050.left.bed ${breakpoint_directory}/D5.DEL.1000.left.bed ${breakpoint_directory}/D5.DEL.950.left.bed ${breakpoint_directory}/D5.DEL.900.left.bed ${breakpoint_directory}/D5.DEL.850.left.bed ${breakpoint_directory}/D5.DEL.800.left.bed ${breakpoint_directory}/D5.DEL.750.left.bed ${breakpoint_directory}/D5.DEL.700.left.bed ${breakpoint_directory}/D5.DEL.650.left.bed ${breakpoint_directory}/D5.DEL.600.left.bed ${breakpoint_directory}/D5.DEL.550.left.bed ${breakpoint_directory}/D5.DEL.500.left.bed ${breakpoint_directory}/D5.DEL.450.left.bed ${breakpoint_directory}/D5.DEL.400.left.bed ${breakpoint_directory}/D5.DEL.350.left.bed ${breakpoint_directory}/D5.DEL.300.left.bed ${breakpoint_directory}/D5.DEL.250.left.bed ${breakpoint_directory}/D5.DEL.200.left.bed ${breakpoint_directory}/D5.DEL.150.left.bed ${breakpoint_directory}/D5.DEL.100.left.bed ${breakpoint_directory}/D5.DEL.50.left.bed ${breakpoint_directory}/D5.DEL.50.right.bed ${breakpoint_directory}/D5.DEL.100.right.bed ${breakpoint_directory}/D5.DEL.150.right.bed ${breakpoint_directory}/D5.DEL.200.right.bed ${breakpoint_directory}/D5.DEL.250.right.bed ${breakpoint_directory}/D5.DEL.300.right.bed ${breakpoint_directory}/D5.DEL.350.right.bed ${breakpoint_directory}/D5.DEL.400.right.bed ${breakpoint_directory}/D5.DEL.450.right.bed ${breakpoint_directory}/D5.DEL.500.right.bed ${breakpoint_directory}/D5.DEL.550.right.bed ${breakpoint_directory}/D5.DEL.600.right.bed ${breakpoint_directory}/D5.DEL.650.right.bed ${breakpoint_directory}/D5.DEL.700.right.bed ${breakpoint_directory}/D5.DEL.750.right.bed ${breakpoint_directory}/D5.DEL.800.right.bed ${breakpoint_directory}/D5.DEL.850.right.bed ${breakpoint_directory}/D5.DEL.900.right.bed ${breakpoint_directory}/D5.DEL.950.right.bed ${breakpoint_directory}/D5.DEL.1000.right.bed ${breakpoint_directory}/D5.DEL.1050.right.bed ${breakpoint_directory}/D5.DEL.1100.right.bed ${breakpoint_directory}/D5.DEL.1150.right.bed ${breakpoint_directory}/D5.DEL.1200.right.bed ${breakpoint_directory}/D5.DEL.1250.right.bed ${breakpoint_directory}/D5.DEL.1300.right.bed ${breakpoint_directory}/D5.DEL.1350.right.bed ${breakpoint_directory}/D5.DEL.1400.right.bed ${breakpoint_directory}/D5.DEL.1450.right.bed ${breakpoint_directory}/D5.DEL.1500.right.bed > ${sample_name}.DEL.filtered.txt

  18. 

  19. # INS

  20. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${filtered_bed} -files ${breakpoint_directory}/D5.INS.1500.left.bed ${breakpoint_directory}/D5.INS.1450.left.bed ${breakpoint_directory}/D5.INS.1400.left.bed ${breakpoint_directory}/D5.INS.1350.left.bed ${breakpoint_directory}/D5.INS.1300.left.bed ${breakpoint_directory}/D5.INS.1250.left.bed ${breakpoint_directory}/D5.INS.1200.left.bed ${breakpoint_directory}/D5.INS.1150.left.bed ${breakpoint_directory}/D5.INS.1100.left.bed ${breakpoint_directory}/D5.INS.1050.left.bed ${breakpoint_directory}/D5.INS.1000.left.bed ${breakpoint_directory}/D5.INS.950.left.bed ${breakpoint_directory}/D5.INS.900.left.bed ${breakpoint_directory}/D5.INS.850.left.bed ${breakpoint_directory}/D5.INS.800.left.bed ${breakpoint_directory}/D5.INS.750.left.bed ${breakpoint_directory}/D5.INS.700.left.bed ${breakpoint_directory}/D5.INS.650.left.bed ${breakpoint_directory}/D5.INS.600.left.bed ${breakpoint_directory}/D5.INS.550.left.bed ${breakpoint_directory}/D5.INS.500.left.bed ${breakpoint_directory}/D5.INS.450.left.bed ${breakpoint_directory}/D5.INS.400.left.bed ${breakpoint_directory}/D5.INS.350.left.bed ${breakpoint_directory}/D5.INS.300.left.bed ${breakpoint_directory}/D5.INS.250.left.bed ${breakpoint_directory}/D5.INS.200.left.bed ${breakpoint_directory}/D5.INS.150.left.bed ${breakpoint_directory}/D5.INS.100.left.bed ${breakpoint_directory}/D5.INS.50.left.bed ${breakpoint_directory}/D5.INS.50.right.bed ${breakpoint_directory}/D5.INS.100.right.bed ${breakpoint_directory}/D5.INS.150.right.bed ${breakpoint_directory}/D5.INS.200.right.bed ${breakpoint_directory}/D5.INS.250.right.bed ${breakpoint_directory}/D5.INS.300.right.bed ${breakpoint_directory}/D5.INS.350.right.bed ${breakpoint_directory}/D5.INS.400.right.bed ${breakpoint_directory}/D5.INS.450.right.bed ${breakpoint_directory}/D5.INS.500.right.bed ${breakpoint_directory}/D5.INS.550.right.bed ${breakpoint_directory}/D5.INS.600.right.bed ${breakpoint_directory}/D5.INS.650.right.bed ${breakpoint_directory}/D5.INS.700.right.bed ${breakpoint_directory}/D5.INS.750.right.bed ${breakpoint_directory}/D5.INS.800.right.bed ${breakpoint_directory}/D5.INS.850.right.bed ${breakpoint_directory}/D5.INS.900.right.bed ${breakpoint_directory}/D5.INS.950.right.bed ${breakpoint_directory}/D5.INS.1000.right.bed ${breakpoint_directory}/D5.INS.1050.right.bed ${breakpoint_directory}/D5.INS.1100.right.bed ${breakpoint_directory}/D5.INS.1150.right.bed ${breakpoint_directory}/D5.INS.1200.right.bed ${breakpoint_directory}/D5.INS.1250.right.bed ${breakpoint_directory}/D5.INS.1300.right.bed ${breakpoint_directory}/D5.INS.1350.right.bed ${breakpoint_directory}/D5.INS.1400.right.bed ${breakpoint_directory}/D5.INS.1450.right.bed ${breakpoint_directory}/D5.INS.1500.right.bed > ${sample_name}.INS.filtered.txt

  21. 

  22. # INV

  23. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${filtered_bed} -files ${breakpoint_directory}/D5.INV.1500.left.bed ${breakpoint_directory}/D5.INV.1450.left.bed ${breakpoint_directory}/D5.INV.1400.left.bed ${breakpoint_directory}/D5.INV.1350.left.bed ${breakpoint_directory}/D5.INV.1300.left.bed ${breakpoint_directory}/D5.INV.1250.left.bed ${breakpoint_directory}/D5.INV.1200.left.bed ${breakpoint_directory}/D5.INV.1150.left.bed ${breakpoint_directory}/D5.INV.1100.left.bed ${breakpoint_directory}/D5.INV.1050.left.bed ${breakpoint_directory}/D5.INV.1000.left.bed ${breakpoint_directory}/D5.INV.950.left.bed ${breakpoint_directory}/D5.INV.900.left.bed ${breakpoint_directory}/D5.INV.850.left.bed ${breakpoint_directory}/D5.INV.800.left.bed ${breakpoint_directory}/D5.INV.750.left.bed ${breakpoint_directory}/D5.INV.700.left.bed ${breakpoint_directory}/D5.INV.650.left.bed ${breakpoint_directory}/D5.INV.600.left.bed ${breakpoint_directory}/D5.INV.550.left.bed ${breakpoint_directory}/D5.INV.500.left.bed ${breakpoint_directory}/D5.INV.450.left.bed ${breakpoint_directory}/D5.INV.400.left.bed ${breakpoint_directory}/D5.INV.350.left.bed ${breakpoint_directory}/D5.INV.300.left.bed ${breakpoint_directory}/D5.INV.250.left.bed ${breakpoint_directory}/D5.INV.200.left.bed ${breakpoint_directory}/D5.INV.150.left.bed ${breakpoint_directory}/D5.INV.100.left.bed ${breakpoint_directory}/D5.INV.50.left.bed ${breakpoint_directory}/D5.INV.50.right.bed ${breakpoint_directory}/D5.INV.100.right.bed ${breakpoint_directory}/D5.INV.150.right.bed ${breakpoint_directory}/D5.INV.200.right.bed ${breakpoint_directory}/D5.INV.250.right.bed ${breakpoint_directory}/D5.INV.300.right.bed ${breakpoint_directory}/D5.INV.350.right.bed ${breakpoint_directory}/D5.INV.400.right.bed ${breakpoint_directory}/D5.INV.450.right.bed ${breakpoint_directory}/D5.INV.500.right.bed ${breakpoint_directory}/D5.INV.550.right.bed ${breakpoint_directory}/D5.INV.600.right.bed ${breakpoint_directory}/D5.INV.650.right.bed ${breakpoint_directory}/D5.INV.700.right.bed ${breakpoint_directory}/D5.INV.750.right.bed ${breakpoint_directory}/D5.INV.800.right.bed ${breakpoint_directory}/D5.INV.850.right.bed ${breakpoint_directory}/D5.INV.900.right.bed ${breakpoint_directory}/D5.INV.950.right.bed ${breakpoint_directory}/D5.INV.1000.right.bed ${breakpoint_directory}/D5.INV.1050.right.bed ${breakpoint_directory}/D5.INV.1100.right.bed ${breakpoint_directory}/D5.INV.1150.right.bed ${breakpoint_directory}/D5.INV.1200.right.bed ${breakpoint_directory}/D5.INV.1250.right.bed ${breakpoint_directory}/D5.INV.1300.right.bed ${breakpoint_directory}/D5.INV.1350.right.bed ${breakpoint_directory}/D5.INV.1400.right.bed ${breakpoint_directory}/D5.INV.1450.right.bed ${breakpoint_directory}/D5.INV.1500.right.bed > ${sample_name}.INV.filtered.txt

  24. 

  25. # DUP

  26. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${filtered_bed} -files ${breakpoint_directory}/D5.DUP.1500.left.bed ${breakpoint_directory}/D5.DUP.1450.left.bed ${breakpoint_directory}/D5.DUP.1400.left.bed ${breakpoint_directory}/D5.DUP.1350.left.bed ${breakpoint_directory}/D5.DUP.1300.left.bed ${breakpoint_directory}/D5.DUP.1250.left.bed ${breakpoint_directory}/D5.DUP.1200.left.bed ${breakpoint_directory}/D5.DUP.1150.left.bed ${breakpoint_directory}/D5.DUP.1100.left.bed ${breakpoint_directory}/D5.DUP.1050.left.bed ${breakpoint_directory}/D5.DUP.1000.left.bed ${breakpoint_directory}/D5.DUP.950.left.bed ${breakpoint_directory}/D5.DUP.900.left.bed ${breakpoint_directory}/D5.DUP.850.left.bed ${breakpoint_directory}/D5.DUP.800.left.bed ${breakpoint_directory}/D5.DUP.750.left.bed ${breakpoint_directory}/D5.DUP.700.left.bed ${breakpoint_directory}/D5.DUP.650.left.bed ${breakpoint_directory}/D5.DUP.600.left.bed ${breakpoint_directory}/D5.DUP.550.left.bed ${breakpoint_directory}/D5.DUP.500.left.bed ${breakpoint_directory}/D5.DUP.450.left.bed ${breakpoint_directory}/D5.DUP.400.left.bed ${breakpoint_directory}/D5.DUP.350.left.bed ${breakpoint_directory}/D5.DUP.300.left.bed ${breakpoint_directory}/D5.DUP.250.left.bed ${breakpoint_directory}/D5.DUP.200.left.bed ${breakpoint_directory}/D5.DUP.150.left.bed ${breakpoint_directory}/D5.DUP.100.left.bed ${breakpoint_directory}/D5.DUP.50.left.bed ${breakpoint_directory}/D5.DUP.50.right.bed ${breakpoint_directory}/D5.DUP.100.right.bed ${breakpoint_directory}/D5.DUP.150.right.bed ${breakpoint_directory}/D5.DUP.200.right.bed ${breakpoint_directory}/D5.DUP.250.right.bed ${breakpoint_directory}/D5.DUP.300.right.bed ${breakpoint_directory}/D5.DUP.350.right.bed ${breakpoint_directory}/D5.DUP.400.right.bed ${breakpoint_directory}/D5.DUP.450.right.bed ${breakpoint_directory}/D5.DUP.500.right.bed ${breakpoint_directory}/D5.DUP.550.right.bed ${breakpoint_directory}/D5.DUP.600.right.bed ${breakpoint_directory}/D5.DUP.650.right.bed ${breakpoint_directory}/D5.DUP.700.right.bed ${breakpoint_directory}/D5.DUP.750.right.bed ${breakpoint_directory}/D5.DUP.800.right.bed ${breakpoint_directory}/D5.DUP.850.right.bed ${breakpoint_directory}/D5.DUP.900.right.bed ${breakpoint_directory}/D5.DUP.950.right.bed ${breakpoint_directory}/D5.DUP.1000.right.bed ${breakpoint_directory}/D5.DUP.1050.right.bed ${breakpoint_directory}/D5.DUP.1100.right.bed ${breakpoint_directory}/D5.DUP.1150.right.bed ${breakpoint_directory}/D5.DUP.1200.right.bed ${breakpoint_directory}/D5.DUP.1250.right.bed ${breakpoint_directory}/D5.DUP.1300.right.bed ${breakpoint_directory}/D5.DUP.1350.right.bed ${breakpoint_directory}/D5.DUP.1400.right.bed ${breakpoint_directory}/D5.DUP.1450.right.bed ${breakpoint_directory}/D5.DUP.1500.right.bed > ${sample_name}.DUP.filtered.txt

  27. 

  28. 

  29. # voted

  30. # BND

  31. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${voted_bed} -files ${breakpoint_directory}/D5.BND.1500.left.bed ${breakpoint_directory}/D5.BND.1450.left.bed ${breakpoint_directory}/D5.BND.1400.left.bed ${breakpoint_directory}/D5.BND.1350.left.bed ${breakpoint_directory}/D5.BND.1300.left.bed ${breakpoint_directory}/D5.BND.1250.left.bed ${breakpoint_directory}/D5.BND.1200.left.bed ${breakpoint_directory}/D5.BND.1150.left.bed ${breakpoint_directory}/D5.BND.1100.left.bed ${breakpoint_directory}/D5.BND.1050.left.bed ${breakpoint_directory}/D5.BND.1000.left.bed ${breakpoint_directory}/D5.BND.950.left.bed ${breakpoint_directory}/D5.BND.900.left.bed ${breakpoint_directory}/D5.BND.850.left.bed ${breakpoint_directory}/D5.BND.800.left.bed ${breakpoint_directory}/D5.BND.750.left.bed ${breakpoint_directory}/D5.BND.700.left.bed ${breakpoint_directory}/D5.BND.650.left.bed ${breakpoint_directory}/D5.BND.600.left.bed ${breakpoint_directory}/D5.BND.550.left.bed ${breakpoint_directory}/D5.BND.500.left.bed ${breakpoint_directory}/D5.BND.450.left.bed ${breakpoint_directory}/D5.BND.400.left.bed ${breakpoint_directory}/D5.BND.350.left.bed ${breakpoint_directory}/D5.BND.300.left.bed ${breakpoint_directory}/D5.BND.250.left.bed ${breakpoint_directory}/D5.BND.200.left.bed ${breakpoint_directory}/D5.BND.150.left.bed ${breakpoint_directory}/D5.BND.100.left.bed ${breakpoint_directory}/D5.BND.50.left.bed ${breakpoint_directory}/D5.BND.50.right.bed ${breakpoint_directory}/D5.BND.100.right.bed ${breakpoint_directory}/D5.BND.150.right.bed ${breakpoint_directory}/D5.BND.200.right.bed ${breakpoint_directory}/D5.BND.250.right.bed ${breakpoint_directory}/D5.BND.300.right.bed ${breakpoint_directory}/D5.BND.350.right.bed ${breakpoint_directory}/D5.BND.400.right.bed ${breakpoint_directory}/D5.BND.450.right.bed ${breakpoint_directory}/D5.BND.500.right.bed ${breakpoint_directory}/D5.BND.550.right.bed ${breakpoint_directory}/D5.BND.600.right.bed ${breakpoint_directory}/D5.BND.650.right.bed ${breakpoint_directory}/D5.BND.700.right.bed ${breakpoint_directory}/D5.BND.750.right.bed ${breakpoint_directory}/D5.BND.800.right.bed ${breakpoint_directory}/D5.BND.850.right.bed ${breakpoint_directory}/D5.BND.900.right.bed ${breakpoint_directory}/D5.BND.950.right.bed ${breakpoint_directory}/D5.BND.1000.right.bed ${breakpoint_directory}/D5.BND.1050.right.bed ${breakpoint_directory}/D5.BND.1100.right.bed ${breakpoint_directory}/D5.BND.1150.right.bed ${breakpoint_directory}/D5.BND.1200.right.bed ${breakpoint_directory}/D5.BND.1250.right.bed ${breakpoint_directory}/D5.BND.1300.right.bed ${breakpoint_directory}/D5.BND.1350.right.bed ${breakpoint_directory}/D5.BND.1400.right.bed ${breakpoint_directory}/D5.BND.1450.right.bed ${breakpoint_directory}/D5.BND.1500.right.bed > ${sample_name}.BND.voted.txt

  32. 

  33. # DEL

  34. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${voted_bed} -files ${breakpoint_directory}/D5.DEL.1500.left.bed ${breakpoint_directory}/D5.DEL.1450.left.bed ${breakpoint_directory}/D5.DEL.1400.left.bed ${breakpoint_directory}/D5.DEL.1350.left.bed ${breakpoint_directory}/D5.DEL.1300.left.bed ${breakpoint_directory}/D5.DEL.1250.left.bed ${breakpoint_directory}/D5.DEL.1200.left.bed ${breakpoint_directory}/D5.DEL.1150.left.bed ${breakpoint_directory}/D5.DEL.1100.left.bed ${breakpoint_directory}/D5.DEL.1050.left.bed ${breakpoint_directory}/D5.DEL.1000.left.bed ${breakpoint_directory}/D5.DEL.950.left.bed ${breakpoint_directory}/D5.DEL.900.left.bed ${breakpoint_directory}/D5.DEL.850.left.bed ${breakpoint_directory}/D5.DEL.800.left.bed ${breakpoint_directory}/D5.DEL.750.left.bed ${breakpoint_directory}/D5.DEL.700.left.bed ${breakpoint_directory}/D5.DEL.650.left.bed ${breakpoint_directory}/D5.DEL.600.left.bed ${breakpoint_directory}/D5.DEL.550.left.bed ${breakpoint_directory}/D5.DEL.500.left.bed ${breakpoint_directory}/D5.DEL.450.left.bed ${breakpoint_directory}/D5.DEL.400.left.bed ${breakpoint_directory}/D5.DEL.350.left.bed ${breakpoint_directory}/D5.DEL.300.left.bed ${breakpoint_directory}/D5.DEL.250.left.bed ${breakpoint_directory}/D5.DEL.200.left.bed ${breakpoint_directory}/D5.DEL.150.left.bed ${breakpoint_directory}/D5.DEL.100.left.bed ${breakpoint_directory}/D5.DEL.50.left.bed ${breakpoint_directory}/D5.DEL.50.right.bed ${breakpoint_directory}/D5.DEL.100.right.bed ${breakpoint_directory}/D5.DEL.150.right.bed ${breakpoint_directory}/D5.DEL.200.right.bed ${breakpoint_directory}/D5.DEL.250.right.bed ${breakpoint_directory}/D5.DEL.300.right.bed ${breakpoint_directory}/D5.DEL.350.right.bed ${breakpoint_directory}/D5.DEL.400.right.bed ${breakpoint_directory}/D5.DEL.450.right.bed ${breakpoint_directory}/D5.DEL.500.right.bed ${breakpoint_directory}/D5.DEL.550.right.bed ${breakpoint_directory}/D5.DEL.600.right.bed ${breakpoint_directory}/D5.DEL.650.right.bed ${breakpoint_directory}/D5.DEL.700.right.bed ${breakpoint_directory}/D5.DEL.750.right.bed ${breakpoint_directory}/D5.DEL.800.right.bed ${breakpoint_directory}/D5.DEL.850.right.bed ${breakpoint_directory}/D5.DEL.900.right.bed ${breakpoint_directory}/D5.DEL.950.right.bed ${breakpoint_directory}/D5.DEL.1000.right.bed ${breakpoint_directory}/D5.DEL.1050.right.bed ${breakpoint_directory}/D5.DEL.1100.right.bed ${breakpoint_directory}/D5.DEL.1150.right.bed ${breakpoint_directory}/D5.DEL.1200.right.bed ${breakpoint_directory}/D5.DEL.1250.right.bed ${breakpoint_directory}/D5.DEL.1300.right.bed ${breakpoint_directory}/D5.DEL.1350.right.bed ${breakpoint_directory}/D5.DEL.1400.right.bed ${breakpoint_directory}/D5.DEL.1450.right.bed ${breakpoint_directory}/D5.DEL.1500.right.bed > ${sample_name}.DEL.voted.txt

  35. 

  36. # INS

  37. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${voted_bed} -files ${breakpoint_directory}/D5.INS.1500.left.bed ${breakpoint_directory}/D5.INS.1450.left.bed ${breakpoint_directory}/D5.INS.1400.left.bed ${breakpoint_directory}/D5.INS.1350.left.bed ${breakpoint_directory}/D5.INS.1300.left.bed ${breakpoint_directory}/D5.INS.1250.left.bed ${breakpoint_directory}/D5.INS.1200.left.bed ${breakpoint_directory}/D5.INS.1150.left.bed ${breakpoint_directory}/D5.INS.1100.left.bed ${breakpoint_directory}/D5.INS.1050.left.bed ${breakpoint_directory}/D5.INS.1000.left.bed ${breakpoint_directory}/D5.INS.950.left.bed ${breakpoint_directory}/D5.INS.900.left.bed ${breakpoint_directory}/D5.INS.850.left.bed ${breakpoint_directory}/D5.INS.800.left.bed ${breakpoint_directory}/D5.INS.750.left.bed ${breakpoint_directory}/D5.INS.700.left.bed ${breakpoint_directory}/D5.INS.650.left.bed ${breakpoint_directory}/D5.INS.600.left.bed ${breakpoint_directory}/D5.INS.550.left.bed ${breakpoint_directory}/D5.INS.500.left.bed ${breakpoint_directory}/D5.INS.450.left.bed ${breakpoint_directory}/D5.INS.400.left.bed ${breakpoint_directory}/D5.INS.350.left.bed ${breakpoint_directory}/D5.INS.300.left.bed ${breakpoint_directory}/D5.INS.250.left.bed ${breakpoint_directory}/D5.INS.200.left.bed ${breakpoint_directory}/D5.INS.150.left.bed ${breakpoint_directory}/D5.INS.100.left.bed ${breakpoint_directory}/D5.INS.50.left.bed ${breakpoint_directory}/D5.INS.50.right.bed ${breakpoint_directory}/D5.INS.100.right.bed ${breakpoint_directory}/D5.INS.150.right.bed ${breakpoint_directory}/D5.INS.200.right.bed ${breakpoint_directory}/D5.INS.250.right.bed ${breakpoint_directory}/D5.INS.300.right.bed ${breakpoint_directory}/D5.INS.350.right.bed ${breakpoint_directory}/D5.INS.400.right.bed ${breakpoint_directory}/D5.INS.450.right.bed ${breakpoint_directory}/D5.INS.500.right.bed ${breakpoint_directory}/D5.INS.550.right.bed ${breakpoint_directory}/D5.INS.600.right.bed ${breakpoint_directory}/D5.INS.650.right.bed ${breakpoint_directory}/D5.INS.700.right.bed ${breakpoint_directory}/D5.INS.750.right.bed ${breakpoint_directory}/D5.INS.800.right.bed ${breakpoint_directory}/D5.INS.850.right.bed ${breakpoint_directory}/D5.INS.900.right.bed ${breakpoint_directory}/D5.INS.950.right.bed ${breakpoint_directory}/D5.INS.1000.right.bed ${breakpoint_directory}/D5.INS.1050.right.bed ${breakpoint_directory}/D5.INS.1100.right.bed ${breakpoint_directory}/D5.INS.1150.right.bed ${breakpoint_directory}/D5.INS.1200.right.bed ${breakpoint_directory}/D5.INS.1250.right.bed ${breakpoint_directory}/D5.INS.1300.right.bed ${breakpoint_directory}/D5.INS.1350.right.bed ${breakpoint_directory}/D5.INS.1400.right.bed ${breakpoint_directory}/D5.INS.1450.right.bed ${breakpoint_directory}/D5.INS.1500.right.bed > ${sample_name}.INS.voted.txt

  38. 

  39. # INV

  40. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${voted_bed} -files ${breakpoint_directory}/D5.INV.1500.left.bed ${breakpoint_directory}/D5.INV.1450.left.bed ${breakpoint_directory}/D5.INV.1400.left.bed ${breakpoint_directory}/D5.INV.1350.left.bed ${breakpoint_directory}/D5.INV.1300.left.bed ${breakpoint_directory}/D5.INV.1250.left.bed ${breakpoint_directory}/D5.INV.1200.left.bed ${breakpoint_directory}/D5.INV.1150.left.bed ${breakpoint_directory}/D5.INV.1100.left.bed ${breakpoint_directory}/D5.INV.1050.left.bed ${breakpoint_directory}/D5.INV.1000.left.bed ${breakpoint_directory}/D5.INV.950.left.bed ${breakpoint_directory}/D5.INV.900.left.bed ${breakpoint_directory}/D5.INV.850.left.bed ${breakpoint_directory}/D5.INV.800.left.bed ${breakpoint_directory}/D5.INV.750.left.bed ${breakpoint_directory}/D5.INV.700.left.bed ${breakpoint_directory}/D5.INV.650.left.bed ${breakpoint_directory}/D5.INV.600.left.bed ${breakpoint_directory}/D5.INV.550.left.bed ${breakpoint_directory}/D5.INV.500.left.bed ${breakpoint_directory}/D5.INV.450.left.bed ${breakpoint_directory}/D5.INV.400.left.bed ${breakpoint_directory}/D5.INV.350.left.bed ${breakpoint_directory}/D5.INV.300.left.bed ${breakpoint_directory}/D5.INV.250.left.bed ${breakpoint_directory}/D5.INV.200.left.bed ${breakpoint_directory}/D5.INV.150.left.bed ${breakpoint_directory}/D5.INV.100.left.bed ${breakpoint_directory}/D5.INV.50.left.bed ${breakpoint_directory}/D5.INV.50.right.bed ${breakpoint_directory}/D5.INV.100.right.bed ${breakpoint_directory}/D5.INV.150.right.bed ${breakpoint_directory}/D5.INV.200.right.bed ${breakpoint_directory}/D5.INV.250.right.bed ${breakpoint_directory}/D5.INV.300.right.bed ${breakpoint_directory}/D5.INV.350.right.bed ${breakpoint_directory}/D5.INV.400.right.bed ${breakpoint_directory}/D5.INV.450.right.bed ${breakpoint_directory}/D5.INV.500.right.bed ${breakpoint_directory}/D5.INV.550.right.bed ${breakpoint_directory}/D5.INV.600.right.bed ${breakpoint_directory}/D5.INV.650.right.bed ${breakpoint_directory}/D5.INV.700.right.bed ${breakpoint_directory}/D5.INV.750.right.bed ${breakpoint_directory}/D5.INV.800.right.bed ${breakpoint_directory}/D5.INV.850.right.bed ${breakpoint_directory}/D5.INV.900.right.bed ${breakpoint_directory}/D5.INV.950.right.bed ${breakpoint_directory}/D5.INV.1000.right.bed ${breakpoint_directory}/D5.INV.1050.right.bed ${breakpoint_directory}/D5.INV.1100.right.bed ${breakpoint_directory}/D5.INV.1150.right.bed ${breakpoint_directory}/D5.INV.1200.right.bed ${breakpoint_directory}/D5.INV.1250.right.bed ${breakpoint_directory}/D5.INV.1300.right.bed ${breakpoint_directory}/D5.INV.1350.right.bed ${breakpoint_directory}/D5.INV.1400.right.bed ${breakpoint_directory}/D5.INV.1450.right.bed ${breakpoint_directory}/D5.INV.1500.right.bed > ${sample_name}.INV.voted.txt

  41. 

  42. # DUP

  43. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${voted_bed} -files ${breakpoint_directory}/D5.DUP.1500.left.bed ${breakpoint_directory}/D5.DUP.1450.left.bed ${breakpoint_directory}/D5.DUP.1400.left.bed ${breakpoint_directory}/D5.DUP.1350.left.bed ${breakpoint_directory}/D5.DUP.1300.left.bed ${breakpoint_directory}/D5.DUP.1250.left.bed ${breakpoint_directory}/D5.DUP.1200.left.bed ${breakpoint_directory}/D5.DUP.1150.left.bed ${breakpoint_directory}/D5.DUP.1100.left.bed ${breakpoint_directory}/D5.DUP.1050.left.bed ${breakpoint_directory}/D5.DUP.1000.left.bed ${breakpoint_directory}/D5.DUP.950.left.bed ${breakpoint_directory}/D5.DUP.900.left.bed ${breakpoint_directory}/D5.DUP.850.left.bed ${breakpoint_directory}/D5.DUP.800.left.bed ${breakpoint_directory}/D5.DUP.750.left.bed ${breakpoint_directory}/D5.DUP.700.left.bed ${breakpoint_directory}/D5.DUP.650.left.bed ${breakpoint_directory}/D5.DUP.600.left.bed ${breakpoint_directory}/D5.DUP.550.left.bed ${breakpoint_directory}/D5.DUP.500.left.bed ${breakpoint_directory}/D5.DUP.450.left.bed ${breakpoint_directory}/D5.DUP.400.left.bed ${breakpoint_directory}/D5.DUP.350.left.bed ${breakpoint_directory}/D5.DUP.300.left.bed ${breakpoint_directory}/D5.DUP.250.left.bed ${breakpoint_directory}/D5.DUP.200.left.bed ${breakpoint_directory}/D5.DUP.150.left.bed ${breakpoint_directory}/D5.DUP.100.left.bed ${breakpoint_directory}/D5.DUP.50.left.bed ${breakpoint_directory}/D5.DUP.50.right.bed ${breakpoint_directory}/D5.DUP.100.right.bed ${breakpoint_directory}/D5.DUP.150.right.bed ${breakpoint_directory}/D5.DUP.200.right.bed ${breakpoint_directory}/D5.DUP.250.right.bed ${breakpoint_directory}/D5.DUP.300.right.bed ${breakpoint_directory}/D5.DUP.350.right.bed ${breakpoint_directory}/D5.DUP.400.right.bed ${breakpoint_directory}/D5.DUP.450.right.bed ${breakpoint_directory}/D5.DUP.500.right.bed ${breakpoint_directory}/D5.DUP.550.right.bed ${breakpoint_directory}/D5.DUP.600.right.bed ${breakpoint_directory}/D5.DUP.650.right.bed ${breakpoint_directory}/D5.DUP.700.right.bed ${breakpoint_directory}/D5.DUP.750.right.bed ${breakpoint_directory}/D5.DUP.800.right.bed ${breakpoint_directory}/D5.DUP.850.right.bed ${breakpoint_directory}/D5.DUP.900.right.bed ${breakpoint_directory}/D5.DUP.950.right.bed ${breakpoint_directory}/D5.DUP.1000.right.bed ${breakpoint_directory}/D5.DUP.1050.right.bed ${breakpoint_directory}/D5.DUP.1100.right.bed ${breakpoint_directory}/D5.DUP.1150.right.bed ${breakpoint_directory}/D5.DUP.1200.right.bed ${breakpoint_directory}/D5.DUP.1250.right.bed ${breakpoint_directory}/D5.DUP.1300.right.bed ${breakpoint_directory}/D5.DUP.1350.right.bed ${breakpoint_directory}/D5.DUP.1400.right.bed ${breakpoint_directory}/D5.DUP.1450.right.bed ${breakpoint_directory}/D5.DUP.1500.right.bed > ${sample_name}.DUP.voted.txt

  44. 

  45. 

  46. 	>>>

  47. 

  48. 	runtime {

  49. 		docker:docker

  50. 		cluster: cluster_config

  51. 		systemDisk: "cloud_ssd 40"

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

  53. 	}

  54. 	output {

  55. 		File filtered_bnd = "${sample_name}.BND.filtered.txt"

  56. 		File filtered_ins = "${sample_name}.INS.filtered.txt"

  57. 		File filtered_inv = "${sample_name}.INV.filtered.txt"

  58. 		File filtered_del = "${sample_name}.DEL.filtered.txt"

  59. 		File filtered_dup = "${sample_name}.DUP.filtered.txt"

  60. 		File voted_bnd = "${sample_name}.BND.voted.txt"

  61. 		File voted_ins = "${sample_name}.INS.voted.txt"

  62. 		File voted_inv = "${sample_name}.INV.voted.txt"

  63. 		File voted_del = "${sample_name}.DEL.voted.txt"

  64. 		File voted_dup = "${sample_name}.DUP.voted.txt"

  65. 	}

  66. }