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

   1 {
   2  "name":"GATK / exome PE fastq to snp",
   3  "components":{
   4   "extract-reference":{
   5    "repository":"arvados",
   6    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
   7    "script":"file-select",
   8    "script_parameters":{
   9     "names":[
  10      "human_g1k_v37.fasta.gz",
  11      "human_g1k_v37.fasta.fai.gz",
  12      "human_g1k_v37.dict.gz"
  13     ],
  14     "input":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi"
  15    },
  16    "output_name":false
  17   },
  18   "bwa-index":{
  19    "repository":"arvados",
  20    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
  21    "script":"bwa-index",
  22    "script_parameters":{
  23     "input":{
  24      "output_of":"extract-reference"
  25     },
  26     "bwa_tbz":{
  27      "value":"8b6e2c4916133e1d859c9e812861ce13+70",
  28      "required":true
  29     }
  30    },
  31    "output_name":false
  32   },
  33   "bwa-aln":{
  34    "repository":"arvados",
  35    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
  36    "script":"bwa-aln",
  37    "script_parameters":{
  38     "input":{
  39      "dataclass":"Collection",
  40      "required":"true"
  41     },
  42     "reference_index":{
  43      "output_of":"bwa-index"
  44     },
  45     "samtools_tgz":{
  46      "value":"c777e23cf13e5d5906abfdc08d84bfdb+74",
  47      "required":true
  48     },
  49     "bwa_tbz":{
  50      "value":"8b6e2c4916133e1d859c9e812861ce13+70",
  51      "required":true
  52     }
  53    },
  54    "runtime_constraints":{
  55     "max_tasks_per_node":1
  56    },
  57    "output_name":false
  58   },
  59   "picard-gatk2-prep":{
  60    "repository":"arvados",
  61    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
  62    "script":"picard-gatk2-prep",
  63    "script_parameters":{
  64     "input":{
  65      "output_of":"bwa-aln"
  66     },
  67     "reference":{
  68      "output_of":"extract-reference"
  69     },
  70     "picard_zip":{
  71      "value":"687f74675c6a0e925dec619cc2bec25f+77",
  72      "required":true
  73     }
  74    },
  75    "runtime_constraints":{
  76     "max_tasks_per_node":1
  77    },
  78    "output_name":false
  79   },
  80   "GATK2-realign":{
  81    "repository":"arvados",
  82    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
  83    "script":"GATK2-realign",
  84    "script_parameters":{
  85     "input":{
  86      "output_of":"picard-gatk2-prep"
  87     },
  88     "gatk_bundle":{
  89      "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
  90      "required":true
  91     },
  92     "picard_zip":{
  93      "value":"687f74675c6a0e925dec619cc2bec25f+77",
  94      "required":true
  95     },
  96     "gatk_tbz":{
  97      "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
  98      "required":true
  99     },
 100     "regions":{
 101      "value":"13b53dbe1ec032dfc495fd974aa5dd4a+87/S02972011_Covered_sort_merged.bed"
 102     },
 103     "region_padding":{
 104      "value":10
 105     }
 106    },
 107    "runtime_constraints":{
 108     "max_tasks_per_node":2
 109    },
 110    "output_name":false
 111   },
 112   "GATK2-bqsr":{
 113    "repository":"arvados",
 114    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
 115    "script":"GATK2-bqsr",
 116    "script_parameters":{
 117     "input":{
 118      "output_of":"GATK2-realign"
 119     },
 120     "gatk_bundle":{
 121      "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
 122      "required":true
 123     },
 124     "picard_zip":{
 125      "value":"687f74675c6a0e925dec619cc2bec25f+77",
 126      "required":true
 127     },
 128     "gatk_tbz":{
 129      "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
 130      "required":true
 131     }
 132    },
 133    "output_name":false
 134   },
 135   "GATK2-merge-call":{
 136    "repository":"arvados",
 137    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
 138    "script":"GATK2-merge-call",
 139    "script_parameters":{
 140     "input":{
 141      "output_of":"GATK2-bqsr"
 142     },
 143     "gatk_bundle":{
 144      "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
 145      "required":true
 146     },
 147     "picard_zip":{
 148      "value":"687f74675c6a0e925dec619cc2bec25f+77",
 149      "required":true
 150     },
 151     "gatk_tbz":{
 152      "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
 153      "required":true
 154     },
 155     "regions":{
 156      "value":"13b53dbe1ec032dfc495fd974aa5dd4a+87/S02972011_Covered_sort_merged.bed"
 157     },
 158     "region_padding":{
 159      "value":10
 160     },
 161     "GATK2_UnifiedGenotyper_args":{
 162      "default":[
 163       "-stand_call_conf",
 164       "30.0",
 165       "-stand_emit_conf",
 166       "30.0",
 167       "-dcov",
 168       "200"
 169      ]
 170     }
 171    },
 172    "output_name":"Variant calls from UnifiedGenotyper"
 173   }
 174  }
 175 }