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", "human_g1k_v37.fasta.fai.gz", "human_g1k_v37.dict.gz"
   9     ],
  10     "input":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi"
  11    },
  12    "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d"
  13   },
  14   "bwa-index":{
  15    "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
  16    "script":"bwa-index",
  17    "script_parameters":{
  18     "input":{
  19      "output_of":"extract-reference"
  20     },
  21     "bwa_tbz":{
  22      "optional":false
  23     }
  24    }
  25   },
  26   "bwa-aln":{
  27    "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
  28    "script":"bwa-aln",
  29    "script_parameters":{
  30     "input":{
  31      "optional":"false"
  32     },
  33     "reference_index":{
  34      "output_of":"bwa-index"
  35     },
  36     "samtools_tgz":{
  37      "optional":false
  38     },
  39     "bwa_tbz":{
  40      "optional":false
  41     }
  42    },
  43    "runtime_constraints":{
  44     "max_tasks_per_node":1
  45    }
  46   },
  47   "picard-gatk2-prep":{
  48    "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
  49    "script":"picard-gatk2-prep",
  50    "script_parameters":{
  51     "input":{
  52       "output_of":"bwa-aln"
  53     },
  54     "reference":{
  55      "output_of":"extract-reference"
  56     },
  57     "picard_zip":{
  58      "optional":false
  59     }
  60    },
  61    "runtime_constraints":{
  62     "max_tasks_per_node":1
  63    }
  64   },
  65   "GATK2-realign":{
  66    "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
  67    "script":"GATK2-realign",
  68    "script_parameters":{
  69     "input":{
  70       "output_of":"picard-gatk2-prep"
  71     },
  72     "gatk_bundle":{
  73      "optional":false
  74     },
  75     "picard_zip":{
  76      "optional":false
  77     },
  78     "gatk_tbz":{
  79      "optional":false
  80     },
  81     "regions":{
  82      "optional":true
  83     },
  84     "region_padding":{
  85      "optional":true
  86     }
  87    },
  88    "runtime_constraints":{
  89     "max_tasks_per_node":2
  90    }
  91   },
  92   "GATK2-bqsr":{
  93    "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
  94    "script":"GATK2-bqsr",
  95    "script_parameters":{
  96     "input":{
  97       "output_of":"GATK2-realign"
  98     },
  99     "gatk_bundle":{
 100      "optional":false
 101     },
 102     "picard_zip":{
 103      "optional":false
 104     },
 105     "gatk_tbz":{
 106      "optional":false
 107     }
 108    }
 109   },
 110   "GATK2-merge-call":{
 111    "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
 112    "script":"GATK2-merge-call",
 113    "script_parameters":{
 114     "input":{
 115       "output_of":"GATK2-bqsr"
 116     },
 117     "gatk_bundle":{
 118      "optional":false
 119     },
 120     "picard_zip":{
 121      "optional":false
 122     },
 123     "gatk_tbz":{
 124      "optional":false
 125     },
 126     "regions":{
 127      "optional":true
 128     },
 129     "region_padding":{
 130      "optional":true
 131     },
 132     "GATK2_UnifiedGenotyper_args":{
 133      "default":["-stand_call_conf","30.0","-stand_emit_conf","30.0","-dcov","200"]
 134     }
 135    }
 136   }
 137  }
 138 }