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high_confidence_calls_intergration
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high_confidence_calls_inter.../workflow.wdl

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  1. import "./tasks/variantsNorm.wdl" as variantsNorm

  2. import "./tasks/mendelian.wdl" as mendelian

  3. import "./tasks/zipIndex.wdl" as zipIndex

  4. import "./tasks/VCFrename.wdl" as VCFrename

  5. import "./tasks/mergeSister.wdl" as mergeSister

  6. import "./tasks/reformVCF.wdl" as reformVCF

  7. import "./tasks/merge.wdl" as merge

  8. import "./tasks/votes.wdl" as votes

  9. 

  10. workflow {{ project_name }} {

  11. 	File inputSamplesFile

  12. 	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)

  13. 	File ref_dir

  14. 	String fasta

  15. 	String cluster_config

  16. 	String disk_size

  17. 

  18. 	scatter (quartet in inputSamples){

  19. 		call variantsNorm.variantsNorm as LCL5variantsNorm{

  20. 			input:

  21. 			vcf=quartet[0],

  22. 			ref_dir=ref_dir,

  23. 			fasta=fasta,

  24. 			sampleName=quartet[4],

  25. 			cluster_config=cluster_config,

  26. 			disk_size=disk_size

  27. 		}

  28. 		call variantsNorm.variantsNorm as LCL6variantsNorm{

  29. 			input:

  30. 			vcf=quartet[1],

  31. 			ref_dir=ref_dir,

  32. 			fasta=fasta,

  33. 			sampleName=quartet[5],

  34. 			cluster_config=cluster_config,

  35. 			disk_size=disk_size

  36. 		}

  37. 		call variantsNorm.variantsNorm as LCL7variantsNorm{

  38. 			input:

  39. 			vcf=quartet[2],

  40. 			ref_dir=ref_dir,

  41. 			fasta=fasta,

  42. 			sampleName=quartet[6],

  43. 			cluster_config=cluster_config,

  44. 			disk_size=disk_size

  45. 		}

  46. 		call variantsNorm.variantsNorm as LCL8variantsNorm{

  47. 			input:

  48. 			vcf=quartet[3],

  49. 			ref_dir=ref_dir,

  50. 			fasta=fasta,

  51. 			sampleName=quartet[7],

  52. 			cluster_config=cluster_config,

  53. 			disk_size=disk_size

  54. 		}

  55. 		call mendelian.mendelian as LCL5mendelian {

  56. 			input:

  57. 			child_vcf=LCL5variantsNorm.normed_vcf,

  58. 			LCL7_vcf=LCL7variantsNorm.normed_vcf,

  59. 			LCL8_vcf=LCL8variantsNorm.normed_vcf,

  60. 			LCL7_name=quartet[6],

  61. 			LCL8_name=quartet[7],

  62. 			child_name=quartet[4],

  63. 			ref_dir=ref_dir,

  64. 			fasta=fasta,

  65. 			cluster_config=cluster_config,

  66. 			disk_size=disk_size

  67. 		}

  68. 		call mendelian.mendelian as LCL6mendelian {

  69. 			input:

  70. 			child_vcf=LCL6variantsNorm.normed_vcf,

  71. 			LCL7_vcf=LCL7variantsNorm.normed_vcf,

  72. 			LCL8_vcf=LCL8variantsNorm.normed_vcf,

  73. 			LCL7_name=quartet[6],

  74. 			LCL8_name=quartet[7],

  75. 			child_name=quartet[5],

  76. 			ref_dir=ref_dir,

  77. 			fasta=fasta,

  78. 			cluster_config=cluster_config,

  79. 			disk_size=disk_size

  80. 		}

  81. 		call zipIndex.zipIndex as LCL5zipIndex {

  82. 			input:

  83. 			vcf=LCL5mendelian.trio_vcf,

  84. 			sample="LCL5",

  85. 			family_name=quartet[8],

  86. 			cluster_config=cluster_config,

  87. 			disk_size=disk_size

  88. 		}

  89. 		call zipIndex.zipIndex as LCL6zipIndex {

  90. 			input:

  91. 			vcf=LCL6mendelian.trio_vcf,

  92. 			sample="LCL6",

  93. 			family_name=quartet[8],

  94. 			cluster_config=cluster_config,

  95. 			disk_size=disk_size

  96. 		}		

  97. 		call VCFrename.VCFrename as LCL5VCFrename {

  98. 			input:

  99. 			trio_vcf_gz=LCL5zipIndex.vcf_gz,

  100. 			trio_vcf_idx=LCL5zipIndex.vcf_idx,

  101. 			mother_name=quartet[7],

  102. 			father_name=quartet[6],

  103. 			child_name=quartet[4],

  104. 			family_name=quartet[8],

  105. 			child="LCL5",

  106. 			cluster_config=cluster_config,

  107. 			disk_size=disk_size

  108. 		}

  109. 		call VCFrename.VCFrename as LCL6VCFrename {

  110. 			input:

  111. 			trio_vcf_gz=LCL6zipIndex.vcf_gz,

  112. 			trio_vcf_idx=LCL6zipIndex.vcf_idx,

  113. 			mother_name=quartet[7],

  114. 			father_name=quartet[6],

  115. 			child_name=quartet[5],

  116. 			family_name=quartet[8],

  117. 			child="LCL6",

  118. 			cluster_config=cluster_config,

  119. 			disk_size=disk_size

  120. 		}

  121. 		call mergeSister.mergeSister as mergeSister {

  122. 			input:

  123. 			LCL5_trio_vcf_gz=LCL5VCFrename.rename_trio_vcf_gz,

  124. 			LCL5_trio_vcf_idx=LCL5VCFrename.rename_trio_vcf_idx,

  125. 			LCL6_trio_vcf_gz=LCL6VCFrename.rename_trio_vcf_gz,

  126. 			LCL6_trio_vcf_idx=LCL6VCFrename.rename_trio_vcf_idx,

  127. 			family_name=quartet[8],

  128. 			cluster_config=cluster_config,

  129. 			disk_size=disk_size

  130. 		}

  131. 		call reformVCF.reformVCF as reformVCF {

  132. 			input:

  133. 			family_mendelian_info=mergeSister.family_mendelian_info,

  134. 			family_name=quartet[8],

  135. 			cluster_config=cluster_config,

  136. 			disk_size=disk_size			

  137. 		}

  138. 		call zipIndex.zipIndex as LCL5familyzipIndex {

  139. 			input:

  140. 			vcf=reformVCF.LCL5_family_info,

  141. 			sample='LCL5',

  142. 			family_name=quartet[8],

  143. 			cluster_config=cluster_config,

  144. 			disk_size=disk_size

  145. 		}

  146. 		call zipIndex.zipIndex as LCL6familyzipIndex {

  147. 			input:

  148. 			vcf=reformVCF.LCL6_family_info,

  149. 			sample='LCL6',

  150. 			family_name=quartet[8],

  151. 			cluster_config=cluster_config,

  152. 			disk_size=disk_size

  153. 		}

  154. 		call zipIndex.zipIndex as LCL7familyzipIndex {

  155. 			input:

  156. 			vcf=reformVCF.LCL7_family_info,

  157. 			sample='LCL7',

  158. 			family_name=quartet[8],

  159. 			cluster_config=cluster_config,

  160. 			disk_size=disk_size

  161. 		}

  162. 		call zipIndex.zipIndex as LCL8familyzipIndex {

  163. 			input:

  164. 			vcf=reformVCF.LCL8_family_info,

  165. 			sample='LCL8',

  166. 			family_name=quartet[8],

  167. 			cluster_config=cluster_config,

  168. 			disk_size=disk_size

  169. 		}		

  170. 	}

  171. 	call merge.merge as LCL5merge {

  172. 		input:

  173. 		family_vcf_gz=LCL5familyzipIndex.vcf_gz,

  174. 		family_vcf_idx=LCL5familyzipIndex.vcf_idx,

  175. 		sample="LCL5",

  176. 		cluster_config=cluster_config,

  177. 		disk_size=disk_size

  178. 	}

  179. 	call votes.votes as LCL5votes{

  180. 		input:

  181. 		merged_vcf=LCL5merge.merged_vcf,

  182. 		vcf_dup=LCL5merge.vcf_dup,

  183. 		sample='LCL5',

  184. 		prefix='LCL5_consensus',

  185. 		cluster_config=cluster_config,

  186. 		disk_size=disk_size

  187. 	}

  188. 	call merge.merge as LCL6merge {

  189. 		input:

  190. 		family_vcf_gz=LCL6familyzipIndex.vcf_gz,

  191. 		family_vcf_idx=LCL6familyzipIndex.vcf_idx,

  192. 		sample="LCL6",

  193. 		cluster_config=cluster_config,

  194. 		disk_size=disk_size

  195. 	}

  196. 	call votes.votes as LCL6votes {

  197. 		input:

  198. 		merged_vcf=LCL6merge.merged_vcf,

  199. 		vcf_dup=LCL6merge.vcf_dup,

  200. 		sample='LCL6',

  201. 		prefix='LCL6_consensus',

  202. 		cluster_config=cluster_config,

  203. 		disk_size=disk_size

  204. 	}

  205. 	call merge.merge as LCL7merge {

  206. 		input:

  207. 		family_vcf_gz=LCL7familyzipIndex.vcf_gz,

  208. 		family_vcf_idx=LCL7familyzipIndex.vcf_idx,

  209. 		sample="LCL7",

  210. 		cluster_config=cluster_config,

  211. 		disk_size=disk_size

  212. 	}

  213. 	call votes.votes as LCL7votes {

  214. 		input:

  215. 		merged_vcf=LCL7merge.merged_vcf,

  216. 		vcf_dup=LCL7merge.vcf_dup,

  217. 		sample='LCL7',

  218. 		prefix='LCL7_consensus',

  219. 		cluster_config=cluster_config,

  220. 		disk_size=disk_size

  221. 	}

  222. 	call merge.merge as LCL8merge {

  223. 		input:

  224. 		family_vcf_gz=LCL8familyzipIndex.vcf_gz,

  225. 		family_vcf_idx=LCL8familyzipIndex.vcf_idx,

  226. 		sample="LCL8",

  227. 		cluster_config=cluster_config,

  228. 		disk_size=disk_size

  229. 	}

  230. 	call votes.votes as LCL8votes {

  231. 		input:

  232. 		merged_vcf=LCL8merge.merged_vcf,

  233. 		vcf_dup=LCL8merge.vcf_dup,

  234. 		sample='LCL8',

  235. 		prefix='LCL8_consensus',

  236. 		cluster_config=cluster_config,

  237. 		disk_size=disk_size

  238. 	}

  239. }