X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/64e7ea7910c797f0339ddd1d5df676b3e53fa9de..c5f67bbc40e8f6a98854b1bf67fc6a98cff80790:/doc/examples/pipeline_templates/gatk-exome-fq-snp.json

diff --git a/doc/examples/pipeline_templates/gatk-exome-fq-snp.json b/doc/examples/pipeline_templates/gatk-exome-fq-snp.json
index 42ba79df81..481dda38ca 100644
--- a/doc/examples/pipeline_templates/gatk-exome-fq-snp.json
+++ b/doc/examples/pipeline_templates/gatk-exome-fq-snp.json
@@ -2,137 +2,174 @@
  "name":"GATK / exome PE fastq to snp",
  "components":{
   "extract-reference":{
+   "repository":"arvados",
+   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"file-select",
    "script_parameters":{
     "names":[
-     "human_g1k_v37.fasta.gz", "human_g1k_v37.fasta.fai.gz", "human_g1k_v37.dict.gz"
+     "human_g1k_v37.fasta.gz",
+     "human_g1k_v37.fasta.fai.gz",
+     "human_g1k_v37.dict.gz"
     ],
     "input":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi"
    },
-   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d"
+   "output_name":false
   },
   "bwa-index":{
-   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+   "repository":"arvados",
+   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"bwa-index",
    "script_parameters":{
     "input":{
      "output_of":"extract-reference"
     },
     "bwa_tbz":{
-     "optional":false
+     "value":"8b6e2c4916133e1d859c9e812861ce13+70",
+     "required":true
     }
-   }
+   },
+   "output_name":false
   },
   "bwa-aln":{
-   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+   "repository":"arvados",
+   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"bwa-aln",
    "script_parameters":{
     "input":{
-     "optional":"false"
+     "dataclass":"Collection",
+     "required":"true"
     },
     "reference_index":{
      "output_of":"bwa-index"
     },
     "samtools_tgz":{
-     "optional":false
+     "value":"c777e23cf13e5d5906abfdc08d84bfdb+74",
+     "required":true
     },
     "bwa_tbz":{
-     "optional":false
+     "value":"8b6e2c4916133e1d859c9e812861ce13+70",
+     "required":true
     }
    },
    "runtime_constraints":{
     "max_tasks_per_node":1
-   }
+   },
+   "output_name":false
   },
   "picard-gatk2-prep":{
-   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+   "repository":"arvados",
+   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"picard-gatk2-prep",
    "script_parameters":{
     "input":{
-      "output_of":"bwa-aln"
+     "output_of":"bwa-aln"
     },
     "reference":{
      "output_of":"extract-reference"
     },
     "picard_zip":{
-     "optional":false
+     "value":"687f74675c6a0e925dec619cc2bec25f+77",
+     "required":true
     }
    },
    "runtime_constraints":{
     "max_tasks_per_node":1
-   }
+   },
+   "output_name":false
   },
   "GATK2-realign":{
-   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+   "repository":"arvados",
+   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"GATK2-realign",
    "script_parameters":{
     "input":{
-      "output_of":"picard-gatk2-prep"
+     "output_of":"picard-gatk2-prep"
     },
     "gatk_bundle":{
-     "optional":false
+     "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
+     "required":true
     },
     "picard_zip":{
-     "optional":false
+     "value":"687f74675c6a0e925dec619cc2bec25f+77",
+     "required":true
     },
     "gatk_tbz":{
-     "optional":false
+     "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
+     "required":true
     },
     "regions":{
-     "optional":true
+     "value":"13b53dbe1ec032dfc495fd974aa5dd4a+87/S02972011_Covered_sort_merged.bed"
     },
     "region_padding":{
-     "optional":true
+     "value":10
     }
    },
    "runtime_constraints":{
     "max_tasks_per_node":2
-   }
+   },
+   "output_name":false
   },
   "GATK2-bqsr":{
-   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+   "repository":"arvados",
+   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"GATK2-bqsr",
    "script_parameters":{
     "input":{
-      "output_of":"GATK2-realign"
+     "output_of":"GATK2-realign"
     },
     "gatk_bundle":{
-     "optional":false
+     "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
+     "required":true
     },
     "picard_zip":{
-     "optional":false
+     "value":"687f74675c6a0e925dec619cc2bec25f+77",
+     "required":true
     },
     "gatk_tbz":{
-     "optional":false
+     "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
+     "required":true
     }
-   }
+   },
+   "output_name":false
   },
   "GATK2-merge-call":{
-   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+   "repository":"arvados",
+   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"GATK2-merge-call",
    "script_parameters":{
     "input":{
-      "output_of":"GATK2-bqsr"
+     "output_of":"GATK2-bqsr"
     },
     "gatk_bundle":{
-     "optional":false
+     "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
+     "required":true
     },
     "picard_zip":{
-     "optional":false
+     "value":"687f74675c6a0e925dec619cc2bec25f+77",
+     "required":true
     },
     "gatk_tbz":{
-     "optional":false
+     "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
+     "required":true
     },
     "regions":{
-     "optional":true
+     "value":"13b53dbe1ec032dfc495fd974aa5dd4a+87/S02972011_Covered_sort_merged.bed"
     },
     "region_padding":{
-     "optional":true
+     "value":10
     },
     "GATK2_UnifiedGenotyper_args":{
-     "default":["-stand_call_conf","30.0","-stand_emit_conf","30.0","-dcov","200"]
+     "default":[
+      "-stand_call_conf",
+      "30.0",
+      "-stand_emit_conf",
+      "30.0",
+      "-dcov",
+      "200"
+     ]
     }
-   }
+   },
+   "output_name":"Variant calls from UnifiedGenotyper"
   }
  }
 }