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    "output_is_persistent":false
  16   },
  17   "bwa-index":{
  18    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
  19    "script":"bwa-index",
  20    "script_parameters":{
  21     "input":{
  22      "output_of":"extract-reference"
  23     },
  24     "bwa_tbz":{
  25      "value":"8b6e2c4916133e1d859c9e812861ce13+70",
  26      "required":true
  27     }
  28    },
  29    "output_is_persistent":false
  30   },
  31   "bwa-aln":{
  32    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
  33    "script":"bwa-aln",
  34    "script_parameters":{
  35     "input":{
  36      "dataclass":"Collection",
  37      "required":"true"
  38     },
  39     "reference_index":{
  40      "output_of":"bwa-index"
  41     },
  42     "samtools_tgz":{
  43      "value":"c777e23cf13e5d5906abfdc08d84bfdb+74",
  44      "required":true
  45     },
  46     "bwa_tbz":{
  47      "value":"8b6e2c4916133e1d859c9e812861ce13+70",
  48      "required":true
  49     }
  50    },
  51    "runtime_constraints":{
  52     "max_tasks_per_node":1
  53    },
  54    "output_is_persistent":false
  55   },
  56   "picard-gatk2-prep":{
  57    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
  58    "script":"picard-gatk2-prep",
  59    "script_parameters":{
  60     "input":{
  61      "output_of":"bwa-aln"
  62     },
  63     "reference":{
  64      "output_of":"extract-reference"
  65     },
  66     "picard_zip":{
  67      "value":"687f74675c6a0e925dec619cc2bec25f+77",
  68      "required":true
  69     }
  70    },
  71    "runtime_constraints":{
  72     "max_tasks_per_node":1
  73    },
  74    "output_is_persistent":false
  75   },
  76   "GATK2-realign":{
  77    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
  78    "script":"GATK2-realign",
  79    "script_parameters":{
  80     "input":{
  81      "output_of":"picard-gatk2-prep"
  82     },
  83     "gatk_bundle":{
  84      "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
  85      "required":true
  86     },
  87     "picard_zip":{
  88      "value":"687f74675c6a0e925dec619cc2bec25f+77",
  89      "required":true
  90     },
  91     "gatk_tbz":{
  92      "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
  93      "required":true
  94     },
  95     "regions":{
  96      "value":"13b53dbe1ec032dfc495fd974aa5dd4a+87/S02972011_Covered_sort_merged.bed"
  97     },
  98     "region_padding":{
  99      "value":10
 100     }
 101    },
 102    "runtime_constraints":{
 103     "max_tasks_per_node":2
 104    },
 105    "output_is_persistent":false
 106   },
 107   "GATK2-bqsr":{
 108    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
 109    "script":"GATK2-bqsr",
 110    "script_parameters":{
 111     "input":{
 112      "output_of":"GATK2-realign"
 113     },
 114     "gatk_bundle":{
 115      "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
 116      "required":true
 117     },
 118     "picard_zip":{
 119      "value":"687f74675c6a0e925dec619cc2bec25f+77",
 120      "required":true
 121     },
 122     "gatk_tbz":{
 123      "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
 124      "required":true
 125     }
 126    },
 127    "output_is_persistent":false
 128   },
 129   "GATK2-merge-call":{
 130    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
 131    "script":"GATK2-merge-call",
 132    "script_parameters":{
 133     "input":{
 134      "output_of":"GATK2-bqsr"
 135     },
 136     "gatk_bundle":{
 137      "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
 138      "required":true
 139     },
 140     "picard_zip":{
 141      "value":"687f74675c6a0e925dec619cc2bec25f+77",
 142      "required":true
 143     },
 144     "gatk_tbz":{
 145      "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
 146      "required":true
 147     },
 148     "regions":{
 149      "value":"13b53dbe1ec032dfc495fd974aa5dd4a+87/S02972011_Covered_sort_merged.bed"
 150     },
 151     "region_padding":{
 152      "value":10
 153     },
 154     "GATK2_UnifiedGenotyper_args":{
 155      "default":[
 156       "-stand_call_conf",
 157       "30.0",
 158       "-stand_emit_conf",
 159       "30.0",
 160       "-dcov",
 161       "200"
 162      ]
 163     }
 164    },
 165    "output_is_persistent":true
 166   }
 167  }
 168 }