Merge branch 'master' into 7492-keepproxy-upstream-errors

[arvados.git] / doc / _includes / _run_command_simple_example.liquid

diff --git a/doc/_includes/_run_command_simple_example.liquid b/doc/_includes/_run_command_simple_example.liquid
index dfa14c954dd5ff12e0c068a7df5db8525c174e60..3f695934aecff49dc71094eb93b6dffa07dc01bb 100644 (file)
--- a/doc/_includes/_run_command_simple_example.liquid
+++ b/doc/_includes/_run_command_simple_example.liquid
@@ -1,25 +1,37 @@
-"bwa-mem": {
-    "script": "run-command",
-    "script_version": "master",
-    "repository": "arvados",
-    "script_parameters": {
-        "command": [
-            "bwa",
-            "mem",
-            "-t",
-            "$(node.cores)",
-            "$(glob $(dir $(reference_collection))/*.fasta)",
-            "$(glob $(dir $(sample))/*_1.fastq)",
-            "$(glob $(dir $(sample))/*_2.fastq)"
-        ],
-        "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
-        "reference_collection": {
-            "required": true,
-            "dataclass": "Collection"
-        },
-        "samples": {
-            "required": true,
-            "dataclass": "Collection"
-        },
+{
+    "name":"run-command example pipeline",
+    "components":{
+         "bwa-mem": {
+            "script": "run-command",
+            "script_version": "master",
+            "repository": "arvados",
+            "script_parameters": {
+                "command": [
+                    "$(dir $(bwa_collection))/bwa",
+                    "mem",
+                    "-t",
+                    "$(node.cores)",
+                    "-R",
+                    "@RG\\\tID:group_id\\\tPL:illumina\\\tSM:sample_id",
+                    "$(glob $(dir $(reference_collection))/*.fasta)",
+                    "$(glob $(dir $(sample))/*_1.fastq)",
+                    "$(glob $(dir $(sample))/*_2.fastq)"
+                ],
+                "reference_collection": {
+                    "required": true,
+                    "dataclass": "Collection"
+                },
+                "bwa_collection": {
+                    "required": true,
+                    "dataclass": "Collection",
+                    "default": "39c6f22d40001074f4200a72559ae7eb+5745"
+                },
+                "sample": {
+                    "required": true,
+                    "dataclass": "Collection"
+                },
+                "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
+            }
+        }
     }
 }