add Real Time Genomics pipeline template

diff --git a/doc/examples/pipeline_templates/rtg-fq-snp.json b/doc/examples/pipeline_templates/rtg-fq-snp.json
new file mode 100644 (file)
index 0000000..1235455
--- /dev/null
+++ b/doc/examples/pipeline_templates/rtg-fq-snp.json
@@ -0,0 +1,76 @@
+{
+ "name":"Real Time Genomics / PE fastq to snp",
+ "components":{
+  "extract_reference":{
+   "script":"file-select",
+   "script_parameters":{
+    "names":[
+     "human_g1k_v37.fasta.gz"
+    ],
+    "input":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi"
+   },
+   "script_version":"4c1f8cd1431ece2ef11c130d48bb2edfd2f00ec2"
+  },
+  "reformat_reference":{
+   "script_version":"4c1f8cd1431ece2ef11c130d48bb2edfd2f00ec2",
+   "script":"rtg-fasta2sdf",
+   "script_parameters":{
+    "input":{
+     "output_of":"extract_reference"
+    },
+    "rtg_binary_zip":"5d33618193f763b7dc3a3fdfa11d452e+95+K@qr1hi",
+    "rtg_license":{
+     "optional":false
+    }
+   }
+  },
+  "reformat_reads":{
+   "script_version":"4c1f8cd1431ece2ef11c130d48bb2edfd2f00ec2",
+   "script":"rtg-fastq2sdf",
+   "script_parameters":{
+    "input":{
+     "optional":false
+    },
+    "rtg_binary_zip":"5d33618193f763b7dc3a3fdfa11d452e+95+K@qr1hi",
+    "rtg_license":{
+     "optional":false
+    }
+   }
+  },
+  "map_reads":{
+   "script_version":"4c1f8cd1431ece2ef11c130d48bb2edfd2f00ec2",
+   "script":"rtg-map",
+   "script_parameters":{
+    "input":{
+     "output_of":"reformat_reads"
+    },
+    "reference":{
+     "output_of":"reformat_reference"
+    },
+    "rtg_binary_zip":"5d33618193f763b7dc3a3fdfa11d452e+95+K@qr1hi",
+    "rtg_license":{
+     "optional":false
+    }
+   },
+   "resource_limits":{
+    "max_tasks_per_node":1
+   }
+  },
+  "report_snp":{
+   "script_version":"4c1f8cd1431ece2ef11c130d48bb2edfd2f00ec2",
+   "script":"rtg-snp",
+   "script_parameters":{
+    "input":{
+     "output_of":"map_reads"
+    },
+    "reference":{
+     "output_of":"reformat_reference"
+    },
+    "rtg_binary_zip":"5d33618193f763b7dc3a3fdfa11d452e+95+K@qr1hi",
+    "rtg_license":{
+     "optional":false
+    }
+   }
+  }
+ }
+}