From b17f25bf7f27ff7d0288ba7c11c50404ea568892 Mon Sep 17 00:00:00 2001
From: Tom Clegg <tom@clinicalfuture.com>
Date: Tue, 10 Dec 2013 17:37:34 -0800
Subject: [PATCH] Add GATK2 exome fastq->vcf pipeline example

closes #1574
---
 .../pipeline_templates/gatk-exome-fq-snp.json | 138 ++++++++++++++++++
 1 file changed, 138 insertions(+)
 create mode 100644 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
new file mode 100644
index 0000000000..42ba79df81
--- /dev/null
+++ b/doc/examples/pipeline_templates/gatk-exome-fq-snp.json
@@ -0,0 +1,138 @@
+{
+ "name":"GATK / exome PE fastq to snp",
+ "components":{
+  "extract-reference":{
+   "script":"file-select",
+   "script_parameters":{
+    "names":[
+     "human_g1k_v37.fasta.gz", "human_g1k_v37.fasta.fai.gz", "human_g1k_v37.dict.gz"
+    ],
+    "input":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi"
+   },
+   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d"
+  },
+  "bwa-index":{
+   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+   "script":"bwa-index",
+   "script_parameters":{
+    "input":{
+     "output_of":"extract-reference"
+    },
+    "bwa_tbz":{
+     "optional":false
+    }
+   }
+  },
+  "bwa-aln":{
+   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+   "script":"bwa-aln",
+   "script_parameters":{
+    "input":{
+     "optional":"false"
+    },
+    "reference_index":{
+     "output_of":"bwa-index"
+    },
+    "samtools_tgz":{
+     "optional":false
+    },
+    "bwa_tbz":{
+     "optional":false
+    }
+   },
+   "runtime_constraints":{
+    "max_tasks_per_node":1
+   }
+  },
+  "picard-gatk2-prep":{
+   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+   "script":"picard-gatk2-prep",
+   "script_parameters":{
+    "input":{
+      "output_of":"bwa-aln"
+    },
+    "reference":{
+     "output_of":"extract-reference"
+    },
+    "picard_zip":{
+     "optional":false
+    }
+   },
+   "runtime_constraints":{
+    "max_tasks_per_node":1
+   }
+  },
+  "GATK2-realign":{
+   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+   "script":"GATK2-realign",
+   "script_parameters":{
+    "input":{
+      "output_of":"picard-gatk2-prep"
+    },
+    "gatk_bundle":{
+     "optional":false
+    },
+    "picard_zip":{
+     "optional":false
+    },
+    "gatk_tbz":{
+     "optional":false
+    },
+    "regions":{
+     "optional":true
+    },
+    "region_padding":{
+     "optional":true
+    }
+   },
+   "runtime_constraints":{
+    "max_tasks_per_node":2
+   }
+  },
+  "GATK2-bqsr":{
+   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+   "script":"GATK2-bqsr",
+   "script_parameters":{
+    "input":{
+      "output_of":"GATK2-realign"
+    },
+    "gatk_bundle":{
+     "optional":false
+    },
+    "picard_zip":{
+     "optional":false
+    },
+    "gatk_tbz":{
+     "optional":false
+    }
+   }
+  },
+  "GATK2-merge-call":{
+   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+   "script":"GATK2-merge-call",
+   "script_parameters":{
+    "input":{
+      "output_of":"GATK2-bqsr"
+    },
+    "gatk_bundle":{
+     "optional":false
+    },
+    "picard_zip":{
+     "optional":false
+    },
+    "gatk_tbz":{
+     "optional":false
+    },
+    "regions":{
+     "optional":true
+    },
+    "region_padding":{
+     "optional":true
+    },
+    "GATK2_UnifiedGenotyper_args":{
+     "default":["-stand_call_conf","30.0","-stand_emit_conf","30.0","-dcov","200"]
+    }
+   }
+  }
+ }
+}
-- 
2.30.2