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high_confidence_calls_manuscript
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high_confidence_calls_manus.../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. import "./tasks/bed_annotation.wdl" as bed_annotation

  10. import "./tasks/mergeVCFInfo.wdl" as mergeVCFInfo

  11. 

  12. workflow {{ project_name }} {

  13. 	File inputSamplesFile

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

  15. 	File ref_dir

  16. 	File repeat_bed

  17. 	String fasta

  18. 	String cluster_config

  19. 	String disk_size

  20. 

  21. 	scatter (quartet in inputSamples){

  22. 		call variantsNorm.variantsNorm as LCL5variantsNorm{

  23. 			input:

  24. 			vcf=quartet[0],

  25. 			ref_dir=ref_dir,

  26. 			fasta=fasta,

  27. 			sampleName=quartet[4],

  28. 			cluster_config=cluster_config,

  29. 			disk_size=disk_size

  30. 		}

  31. 		call variantsNorm.variantsNorm as LCL6variantsNorm{

  32. 			input:

  33. 			vcf=quartet[1],

  34. 			ref_dir=ref_dir,

  35. 			fasta=fasta,

  36. 			sampleName=quartet[5],

  37. 			cluster_config=cluster_config,

  38. 			disk_size=disk_size

  39. 		}

  40. 		call variantsNorm.variantsNorm as LCL7variantsNorm{

  41. 			input:

  42. 			vcf=quartet[2],

  43. 			ref_dir=ref_dir,

  44. 			fasta=fasta,

  45. 			sampleName=quartet[6],

  46. 			cluster_config=cluster_config,

  47. 			disk_size=disk_size

  48. 		}

  49. 		call variantsNorm.variantsNorm as LCL8variantsNorm{

  50. 			input:

  51. 			vcf=quartet[3],

  52. 			ref_dir=ref_dir,

  53. 			fasta=fasta,

  54. 			sampleName=quartet[7],

  55. 			cluster_config=cluster_config,

  56. 			disk_size=disk_size

  57. 		}

  58. 		call zipIndex.zipIndex as LCL5normZip{

  59. 			input:

  60. 			vcf=LCL5variantsNorm.normed_vcf,

  61. 			cluster_config=cluster_config,

  62. 			disk_size=disk_size

  63. 		}

  64. 		call zipIndex.zipIndex as LCL6normZip{

  65. 			input:

  66. 			vcf=LCL6variantsNorm.normed_vcf,

  67. 			cluster_config=cluster_config,

  68. 			disk_size=disk_size		

  69. 		}

  70. 		call zipIndex.zipIndex as LCL7normZip{

  71. 			input:

  72. 			vcf=LCL7variantsNorm.normed_vcf,

  73. 			cluster_config=cluster_config,

  74. 			disk_size=disk_size		

  75. 		}

  76. 		call zipIndex.zipIndex as LCL8normZip{

  77. 			input:

  78. 			vcf=LCL8variantsNorm.normed_vcf,

  79. 			cluster_config=cluster_config,

  80. 			disk_size=disk_size		

  81. 		}

  82. 		call mendelian.mendelian as LCL5mendelian {

  83. 			input:

  84. 			child_vcf=LCL5variantsNorm.normed_vcf,

  85. 			LCL7_vcf=LCL7variantsNorm.normed_vcf,

  86. 			LCL8_vcf=LCL8variantsNorm.normed_vcf,

  87. 			LCL7_name=quartet[6],

  88. 			LCL8_name=quartet[7],

  89. 			child_name=quartet[4],

  90. 			ref_dir=ref_dir,

  91. 			fasta=fasta,

  92. 			cluster_config=cluster_config,

  93. 			disk_size=disk_size

  94. 		}

  95. 		call mendelian.mendelian as LCL6mendelian {

  96. 			input:

  97. 			child_vcf=LCL6variantsNorm.normed_vcf,

  98. 			LCL7_vcf=LCL7variantsNorm.normed_vcf,

  99. 			LCL8_vcf=LCL8variantsNorm.normed_vcf,

  100. 			LCL7_name=quartet[6],

  101. 			LCL8_name=quartet[7],

  102. 			child_name=quartet[5],

  103. 			ref_dir=ref_dir,

  104. 			fasta=fasta,

  105. 			cluster_config=cluster_config,

  106. 			disk_size=disk_size

  107. 		}

  108. 		call zipIndex.zipIndex as LCL5zipIndex {

  109. 			input:

  110. 			vcf=LCL5mendelian.trio_vcf,

  111. 			cluster_config=cluster_config,

  112. 			disk_size=disk_size

  113. 		}

  114. 		call zipIndex.zipIndex as LCL6zipIndex {

  115. 			input:

  116. 			vcf=LCL6mendelian.trio_vcf,

  117. 			cluster_config=cluster_config,

  118. 			disk_size=disk_size

  119. 		}		

  120. 		call VCFrename.VCFrename as LCL5VCFrename {

  121. 			input:

  122. 			trio_vcf_gz=LCL5zipIndex.vcf_gz,

  123. 			trio_vcf_idx=LCL5zipIndex.vcf_idx,

  124. 			mother_name=quartet[7],

  125. 			father_name=quartet[6],

  126. 			child_name=quartet[4],

  127. 			family_name=quartet[8],

  128. 			child="LCL5",

  129. 			cluster_config=cluster_config,

  130. 			disk_size=disk_size

  131. 		}

  132. 		call VCFrename.VCFrename as LCL6VCFrename {

  133. 			input:

  134. 			trio_vcf_gz=LCL6zipIndex.vcf_gz,

  135. 			trio_vcf_idx=LCL6zipIndex.vcf_idx,

  136. 			mother_name=quartet[7],

  137. 			father_name=quartet[6],

  138. 			child_name=quartet[5],

  139. 			family_name=quartet[8],

  140. 			child="LCL6",

  141. 			cluster_config=cluster_config,

  142. 			disk_size=disk_size

  143. 		}

  144. 		call mergeSister.mergeSister as mergeSister {

  145. 			input:

  146. 			LCL5_trio_vcf_gz=LCL5VCFrename.rename_trio_vcf_gz,

  147. 			LCL5_trio_vcf_idx=LCL5VCFrename.rename_trio_vcf_idx,

  148. 			LCL6_trio_vcf_gz=LCL6VCFrename.rename_trio_vcf_gz,

  149. 			LCL6_trio_vcf_idx=LCL6VCFrename.rename_trio_vcf_idx,

  150. 			family_name=quartet[8],

  151. 			cluster_config=cluster_config,

  152. 			disk_size=disk_size

  153. 		}

  154. 		call reformVCF.reformVCF as reformVCF {

  155. 			input:

  156. 			family_mendelian_info=mergeSister.family_mendelian_info,

  157. 			family_name=quartet[8],

  158. 			cluster_config=cluster_config,

  159. 			disk_size=disk_size			

  160. 		}

  161. 		call zipIndex.zipIndex as LCL5familyzipIndex {

  162. 			input:

  163. 			vcf=reformVCF.LCL5_family_info,

  164. 			cluster_config=cluster_config,

  165. 			disk_size=disk_size

  166. 		}

  167. 		call zipIndex.zipIndex as LCL6familyzipIndex {

  168. 			input:

  169. 			vcf=reformVCF.LCL6_family_info,

  170. 			cluster_config=cluster_config,

  171. 			disk_size=disk_size

  172. 		}

  173. 		call zipIndex.zipIndex as LCL7familyzipIndex {

  174. 			input:

  175. 			vcf=reformVCF.LCL7_family_info,

  176. 			cluster_config=cluster_config,

  177. 			disk_size=disk_size

  178. 		}

  179. 		call zipIndex.zipIndex as LCL8familyzipIndex {

  180. 			input:

  181. 			vcf=reformVCF.LCL8_family_info,

  182. 			cluster_config=cluster_config,

  183. 			disk_size=disk_size

  184. 		}		

  185. 	}

  186. 	### family info merge

  187. 	call merge.merge as LCL5merge {

  188. 		input:

  189. 		family_vcf_gz=LCL5familyzipIndex.vcf_gz,

  190. 		family_vcf_idx=LCL5familyzipIndex.vcf_idx,

  191. 		sample="LCL5",

  192. 		cluster_config=cluster_config,

  193. 		disk_size=disk_size

  194. 	}

  195. 	call votes.votes as LCL5votes{

  196. 		input:

  197. 		merged_vcf=LCL5merge.merged_vcf,

  198. 		vcf_dup=LCL5merge.vcf_dup,

  199. 		sample='LCL5',

  200. 		prefix='LCL5_consensus',

  201. 		cluster_config=cluster_config,

  202. 		disk_size=disk_size

  203. 	}	

  204. 	call merge.merge as LCL6merge {

  205. 		input:

  206. 		family_vcf_gz=LCL6familyzipIndex.vcf_gz,

  207. 		family_vcf_idx=LCL6familyzipIndex.vcf_idx,

  208. 		sample="LCL6",

  209. 		cluster_config=cluster_config,

  210. 		disk_size=disk_size

  211. 	}

  212. 	call votes.votes as LCL6votes {

  213. 		input:

  214. 		merged_vcf=LCL6merge.merged_vcf,

  215. 		vcf_dup=LCL6merge.vcf_dup,

  216. 		sample='LCL6',

  217. 		prefix='LCL6_consensus',

  218. 		cluster_config=cluster_config,

  219. 		disk_size=disk_size

  220. 	}	

  221. 	call merge.merge as LCL7merge {

  222. 		input:

  223. 		family_vcf_gz=LCL7familyzipIndex.vcf_gz,

  224. 		family_vcf_idx=LCL7familyzipIndex.vcf_idx,

  225. 		sample="LCL7",

  226. 		cluster_config=cluster_config,

  227. 		disk_size=disk_size

  228. 	}

  229. 	call votes.votes as LCL7votes {

  230. 		input:

  231. 		merged_vcf=LCL7merge.merged_vcf,

  232. 		vcf_dup=LCL7merge.vcf_dup,

  233. 		sample='LCL7',

  234. 		prefix='LCL7_consensus',

  235. 		cluster_config=cluster_config,

  236. 		disk_size=disk_size

  237. 	}	

  238. 	call merge.merge as LCL8merge {

  239. 		input:

  240. 		family_vcf_gz=LCL8familyzipIndex.vcf_gz,

  241. 		family_vcf_idx=LCL8familyzipIndex.vcf_idx,

  242. 		sample="LCL8",

  243. 		cluster_config=cluster_config,

  244. 		disk_size=disk_size

  245. 	}

  246. 	call votes.votes as LCL8votes {

  247. 		input:

  248. 		merged_vcf=LCL8merge.merged_vcf,

  249. 		vcf_dup=LCL8merge.vcf_dup,

  250. 		sample='LCL8',

  251. 		prefix='LCL8_consensus',

  252. 		cluster_config=cluster_config,

  253. 		disk_size=disk_size

  254. 	}

  255. 	### vcf original information

  256. 	call mergeVCFInfo.mergeVCFInfo as LCL5mergeVCF {

  257. 		input:

  258. 		vcf_gz=LCL5normZip.vcf_gz,

  259. 		vcf_idx=LCL5normZip.vcf_idx,

  260. 		sample='LCL5',

  261. 		cluster_config=cluster_config,

  262. 		disk_size=disk_size

  263. 	}

  264. 	call bed_annotation.bed_annotation as LCL5bedAnnotation {

  265. 		input:

  266. 		merged_vcf=LCL5mergeVCF.merged_vcf,

  267. 		merged_vcf_idx=LCL5mergeVCF.merged_vcf_idx,

  268. 		repeat_bed=repeat_bed,

  269. 		sample='LCL5',

  270. 		cluster_config=cluster_config,

  271. 		disk_size=disk_size

  272. 	}

  273. 	call mergeVCFInfo.mergeVCFInfo as LCL6mergeVCF {

  274. 		input:

  275. 		vcf_gz=LCL6normZip.vcf_gz,

  276. 		vcf_idx=LCL6normZip.vcf_idx,

  277. 		sample='LCL6',

  278. 		cluster_config=cluster_config,

  279. 		disk_size=disk_size

  280. 	}

  281. 	call bed_annotation.bed_annotation as LCL6bedAnnotation {

  282. 		input:

  283. 		merged_vcf=LCL6mergeVCF.merged_vcf,

  284. 		merged_vcf_idx=LCL6mergeVCF.merged_vcf_idx,

  285. 		repeat_bed=repeat_bed,

  286. 		sample='LCL6',

  287. 		cluster_config=cluster_config,

  288. 		disk_size=disk_size

  289. 	}

  290. 	call mergeVCFInfo.mergeVCFInfo as LCL7mergeVCF {

  291. 		input:

  292. 		vcf_gz=LCL7normZip.vcf_gz,

  293. 		vcf_idx=LCL7normZip.vcf_idx,

  294. 		sample='LCL7',

  295. 		cluster_config=cluster_config,

  296. 		disk_size=disk_size

  297. 	}

  298. 	call bed_annotation.bed_annotation as LCL7bedAnnotation {

  299. 		input:

  300. 		merged_vcf=LCL7mergeVCF.merged_vcf,

  301. 		merged_vcf_idx=LCL7mergeVCF.merged_vcf_idx,

  302. 		repeat_bed=repeat_bed,

  303. 		sample='LCL7',

  304. 		cluster_config=cluster_config,

  305. 		disk_size=disk_size

  306. 	}

  307. 	call mergeVCFInfo.mergeVCFInfo as LCL8mergeVCF {

  308. 		input:

  309. 		vcf_gz=LCL8normZip.vcf_gz,

  310. 		vcf_idx=LCL8normZip.vcf_idx,

  311. 		sample='LCL8',

  312. 		cluster_config=cluster_config,

  313. 		disk_size=disk_size

  314. 	}

  315. 	call bed_annotation.bed_annotation as LCL8bedAnnotation {

  316. 		input:

  317. 		merged_vcf=LCL8mergeVCF.merged_vcf,

  318. 		merged_vcf_idx=LCL8mergeVCF.merged_vcf_idx,

  319. 		repeat_bed=repeat_bed,

  320. 		sample='LCL8',

  321. 		cluster_config=cluster_config,

  322. 		disk_size=disk_size

  323. 	}

  324. }