doc/examples/pipeline_templates/rtg-fq-snp.json

   1 {
   2  "name":"Real Time Genomics / 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     ],
  10     "input":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi"
  11    },
  12    "script_version":"4c1f8cd1431ece2ef11c130d48bb2edfd2f00ec2"
  13   },
  14   "reformat_reference":{
  15    "script_version":"4c1f8cd1431ece2ef11c130d48bb2edfd2f00ec2",
  16    "script":"rtg-fasta2sdf",
  17    "script_parameters":{
  18     "input":{
  19      "output_of":"extract_reference"
  20     },
  21     "rtg_binary_zip":"5d33618193f763b7dc3a3fdfa11d452e+95+K@qr1hi",
  22     "rtg_license":{
  23      "optional":false
  24     }
  25    }
  26   },
  27   "reformat_reads":{
  28    "script_version":"4c1f8cd1431ece2ef11c130d48bb2edfd2f00ec2",
  29    "script":"rtg-fastq2sdf",
  30    "script_parameters":{
  31     "input":{
  32      "optional":false
  33     },
  34     "rtg_binary_zip":"5d33618193f763b7dc3a3fdfa11d452e+95+K@qr1hi",
  35     "rtg_license":{
  36      "optional":false
  37     }
  38    }
  39   },
  40   "map_reads":{
  41    "script_version":"4c1f8cd1431ece2ef11c130d48bb2edfd2f00ec2",
  42    "script":"rtg-map",
  43    "script_parameters":{
  44     "input":{
  45      "output_of":"reformat_reads"
  46     },
  47     "reference":{
  48      "output_of":"reformat_reference"
  49     },
  50     "rtg_binary_zip":"5d33618193f763b7dc3a3fdfa11d452e+95+K@qr1hi",
  51     "rtg_license":{
  52      "optional":false
  53     }
  54    },
  55    "runtime_constraints":{
  56     "max_tasks_per_node":1
  57    }
  58   },
  59   "report_snp":{
  60    "script_version":"4c1f8cd1431ece2ef11c130d48bb2edfd2f00ec2",
  61    "script":"rtg-snp",
  62    "script_parameters":{
  63     "input":{
  64      "output_of":"map_reads"
  65     },
  66     "reference":{
  67      "output_of":"reformat_reference"
  68     },
  69     "rtg_binary_zip":"5d33618193f763b7dc3a3fdfa11d452e+95+K@qr1hi",
  70     "rtg_license":{
  71      "optional":false
  72     }
  73    }
  74   }
  75  }
  76 }