doc/examples/pipeline_templates/gatk-exome-fq-snp.json

   1 {
   2  "name":"GATK / exome PE fastq to snp",
   3  "components":{
   4   "extract-reference":{
   5    "script":"file-select",
   6    "script_parameters":{
   7     "names":[
   8      "human_g1k_v37.fasta.gz",
   9      "human_g1k_v37.fasta.fai.gz",
  10      "human_g1k_v37.dict.gz"
  11     ],
  12     "input":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi"
  13    },
  14    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153"
  15   },
  16   "bwa-index":{
  17    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
  18    "script":"bwa-index",
  19    "script_parameters":{
  20     "input":{
  21      "output_of":"extract-reference"
  22     },
  23     "bwa_tbz":{
  24      "value":"8b6e2c4916133e1d859c9e812861ce13+70",
  25      "required":true
  26     }
  27    }
  28   },
  29   "bwa-aln":{
  30    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
  31    "script":"bwa-aln",
  32    "script_parameters":{
  33     "input":{
  34      "dataclass":"Collection",
  35      "required":"true"
  36     },
  37     "reference_index":{
  38      "output_of":"bwa-index"
  39     },
  40     "samtools_tgz":{
  41      "value":"c777e23cf13e5d5906abfdc08d84bfdb+74",
  42      "required":true
  43     },
  44     "bwa_tbz":{
  45      "value":"8b6e2c4916133e1d859c9e812861ce13+70",
  46      "required":true
  47     }
  48    },
  49    "runtime_constraints":{
  50     "max_tasks_per_node":1
  51    }
  52   },
  53   "picard-gatk2-prep":{
  54    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
  55    "script":"picard-gatk2-prep",
  56    "script_parameters":{
  57     "input":{
  58      "output_of":"bwa-aln"
  59     },
  60     "reference":{
  61      "output_of":"extract-reference"
  62     },
  63     "picard_zip":{
  64      "value":"687f74675c6a0e925dec619cc2bec25f+77",
  65      "required":true
  66     }
  67    },
  68    "runtime_constraints":{
  69     "max_tasks_per_node":1
  70    }
  71   },
  72   "GATK2-realign":{
  73    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
  74    "script":"GATK2-realign",
  75    "script_parameters":{
  76     "input":{
  77      "output_of":"picard-gatk2-prep"
  78     },
  79     "gatk_bundle":{
  80      "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
  81      "required":true
  82     },
  83     "picard_zip":{
  84      "value":"687f74675c6a0e925dec619cc2bec25f+77",
  85      "required":true
  86     },
  87     "gatk_tbz":{
  88      "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
  89      "required":true
  90     },
  91     "regions":{
  92      "value":"13b53dbe1ec032dfc495fd974aa5dd4a+87/S02972011_Covered_sort_merged.bed"
  93     },
  94     "region_padding":{
  95      "value":10
  96     }
  97    },
  98    "runtime_constraints":{
  99     "max_tasks_per_node":2
 100    }
 101   },
 102   "GATK2-bqsr":{
 103    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
 104    "script":"GATK2-bqsr",
 105    "script_parameters":{
 106     "input":{
 107      "output_of":"GATK2-realign"
 108     },
 109     "gatk_bundle":{
 110      "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
 111      "required":true
 112     },
 113     "picard_zip":{
 114      "value":"687f74675c6a0e925dec619cc2bec25f+77",
 115      "required":true
 116     },
 117     "gatk_tbz":{
 118      "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
 119      "required":true
 120     }
 121    }
 122   },
 123   "GATK2-merge-call":{
 124    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
 125    "script":"GATK2-merge-call",
 126    "script_parameters":{
 127     "input":{
 128      "output_of":"GATK2-bqsr"
 129     },
 130     "gatk_bundle":{
 131      "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
 132      "required":true
 133     },
 134     "picard_zip":{
 135      "value":"687f74675c6a0e925dec619cc2bec25f+77",
 136      "required":true
 137     },
 138     "gatk_tbz":{
 139      "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
 140      "required":true
 141     },
 142     "regions":{
 143      "value":"13b53dbe1ec032dfc495fd974aa5dd4a+87/S02972011_Covered_sort_merged.bed"
 144     },
 145     "region_padding":{
 146      "value":10
 147     },
 148     "GATK2_UnifiedGenotyper_args":{
 149      "default":[
 150       "-stand_call_conf",
 151       "30.0",
 152       "-stand_emit_conf",
 153       "30.0",
 154       "-dcov",
 155       "200"
 156      ]
 157     }
 158    }
 159   }
 160  }
 161 }