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3 "annotation": "",
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4 "format-version": "0.1",
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5 "name": "CFSAN SNP Pipeline",
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6 "steps": {
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14 "label": "Reference FASTA",
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15 "name": "Input dataset",
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16 "outputs": [],
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17 "position": {
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24 "type": "data_input",
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25 "uuid": "024fcab7-2daf-4b89-9730-614ee2737db8",
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35 "annotation": "",
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39 "input_connections": {},
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40 "inputs": [],
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41 "label": "Collection of Paired-End Reads",
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42 "name": "Input dataset collection",
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43 "outputs": [],
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44 "position": {
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48 "tool_id": null,
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49 "tool_state": "{\"collection_type\": \"list:paired\"}",
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50 "tool_version": null,
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51 "type": "data_collection_input",
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52 "uuid": "66a18e16-33f7-4488-ac17-508725a58279",
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58 }
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60 },
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61 "2": {
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62 "annotation": "",
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63 "content_id": "map_reads",
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64 "errors": null,
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65 "id": 2,
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66 "input_connections": {
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68 "id": 1,
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71 "source|reference": {
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75 },
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76 "inputs": [
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77 {
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78 "description": "runtime parameter for tool 1. Map Reads",
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79 "name": "source"
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80 },
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81 {
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82 "description": "runtime parameter for tool 1. Map Reads",
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83 "name": "reads"
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84 }
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85 ],
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86 "label": null,
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87 "name": "1. Map Reads",
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88 "outputs": [
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89 {
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90 "name": "align_from_collection",
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91 "type": "sam"
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92 },
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93 {
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94 "name": "align_from_history",
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95 "type": "sam"
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96 },
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97 {
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98 "name": "cache_log",
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99 "type": "txt"
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100 },
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101 {
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102 "name": "ref_out",
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103 "type": "fasta"
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104 }
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105 ],
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106 "position": {
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110 "post_job_actions": {},
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111 "tool_id": "map_reads",
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112 "tool_state": "{\"source\": \"{\\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"source_select\\\": \\\"history\\\"}\", \"reads\": \"{\\\"coll\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"reads_select\\\": \\\"collection\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
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113 "tool_version": "1.0.1",
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114 "type": "tool",
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115 "uuid": "112e11d9-2670-4aae-9bee-3b25e0dd3398",
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116 "workflow_outputs": []
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117 },
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118 "3": {
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119 "annotation": "",
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120 "content_id": "call_sites",
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121 "errors": null,
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122 "id": 3,
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123 "input_connections": {
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124 "input": {
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125 "id": 0,
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126 "output_name": "output"
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127 },
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128 "sample": {
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129 "id": 2,
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130 "output_name": "align_from_collection"
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131 }
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132 },
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133 "inputs": [],
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134 "label": null,
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135 "name": "2. Call Sites",
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136 "outputs": [
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137 {
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138 "name": "calls",
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139 "type": "vcf"
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140 },
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141 {
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142 "name": "pileup",
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143 "type": "pileup"
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144 },
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145 {
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146 "name": "metrics",
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147 "type": "txt"
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148 },
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149 {
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150 "name": "cache_log",
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151 "type": "txt"
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152 }
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158 "post_job_actions": {},
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159 "tool_id": "call_sites",
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160 "tool_state": "{\"sample\": \"{\\\"values\\\": [{\\\"src\\\": \\\"hda\\\", \\\"id\\\": 24}]}\", \"input\": \"{\\\"values\\\": [{\\\"src\\\": \\\"hda\\\", \\\"id\\\": 26}]}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
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164 "workflow_outputs": []
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165 },
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166 "4": {
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167 "annotation": "",
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168 "content_id": "filter_regions",
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169 "errors": null,
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170 "id": 4,
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171 "input_connections": {
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172 "calls": {
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180 },
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181 "inputs": [],
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182 "label": null,
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183 "name": "3. Filter SNP Regions",
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184 "outputs": [
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185 {
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186 "name": "filcalls",
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187 "type": "vcf"
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188 },
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189 {
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190 "name": "excludes",
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207 "annotation": "",
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208 "content_id": "merge_sites",
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209 "errors": null,
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210 "id": 5,
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211 "input_connections": {
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212 "calls": {
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214 "output_name": "calls"
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216 },
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217 "inputs": [
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218 {
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219 "description": "runtime parameter for tool 4. Merge Sites",
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220 "name": "calls"
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221 }
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222 ],
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223 "label": null,
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224 "name": "4. Merge Sites",
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225 "outputs": [
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226 {
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227 "name": "snplist",
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228 "type": "txt"
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240 "action_type": "TagDatasetAction",
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241 "output_name": "snplist"
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250 {
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258 "annotation": "",
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259 "content_id": "merge_sites",
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262 "input_connections": {
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263 "calls": {
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264 "id": 4,
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265 "output_name": "filcalls"
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266 }
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267 },
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268 "inputs": [
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269 {
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270 "description": "runtime parameter for tool 4. Merge Sites",
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271 "name": "calls"
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272 }
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273 ],
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274 "label": null,
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275 "name": "4. Merge Sites",
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276 "outputs": [
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277 {
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278 "name": "snplist",
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279 "type": "txt"
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292 "output_name": "snplist"
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293 }
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295 "tool_id": "merge_sites",
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303 "output_name": "snplist",
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304 "uuid": "ab240b50-625d-4468-90fe-02363974abea"
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305 }
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306 ]
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307 },
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308 "7": {
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309 "annotation": "",
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310 "content_id": "call_consensus",
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311 "errors": null,
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312 "id": 7,
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313 "input_connections": {
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314 "call_pileup": {
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315 "id": 3,
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316 "output_name": "pileup"
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317 },
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318 "calls": {
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319 "id": 3,
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320 "output_name": "calls"
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321 },
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322 "snps": {
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323 "id": 5,
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324 "output_name": "snplist"
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326 },
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327 "inputs": [],
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328 "label": null,
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329 "name": "5. Call consensus SNPs",
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330 "outputs": [
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331 {
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332 "name": "calls_consensus_vcf",
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333 "type": "vcf"
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334 },
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335 {
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336 "name": "calls_consensus_fa",
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337 "type": "fasta"
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339 {
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340 "name": "cache_log",
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341 "type": "txt"
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342 }
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344 "position": {
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346 "top": 707.5
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348 "post_job_actions": {},
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349 "tool_id": "call_consensus",
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350 "tool_state": "{\"snps\": \"{\\\"values\\\": [{\\\"src\\\": \\\"hda\\\", \\\"id\\\": 26}]}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"call_pileup\": \"null\", \"calls\": \"null\"}",
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351 "tool_version": "1.0.1",
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352 "type": "tool",
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