Merge branch '12409-cwl-v1.2' refs #12409

[arvados.git] / 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 f84ad3fb5274ebca31f8dca2c62ba0c5f4b4ebee..481dda38ca70153dd4cda2154e4754a55eef12f2 100644 (file)
--- a/doc/examples/pipeline_templates/gatk-exome-fq-snp.json
+++ b/doc/examples/pipeline_templates/gatk-exome-fq-snp.json
@@ -2,6 +2,8 @@
  "name":"GATK / exome PE fastq to snp",
  "components":{
   "extract-reference":{
+   "repository":"arvados",
+   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"file-select",
    "script_parameters":{
     "names":[
@@ -11,10 +13,10 @@
     ],
     "input":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi"
    },
-   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
-   "output_is_persistent":false
+   "output_name":false
   },
   "bwa-index":{
+   "repository":"arvados",
    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"bwa-index",
    "script_parameters":{
@@ -26,9 +28,10 @@
      "required":true
     }
    },
-   "output_is_persistent":false
+   "output_name":false
   },
   "bwa-aln":{
+   "repository":"arvados",
    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"bwa-aln",
    "script_parameters":{
@@ -51,9 +54,10 @@
    "runtime_constraints":{
     "max_tasks_per_node":1
    },
-   "output_is_persistent":false
+   "output_name":false
   },
   "picard-gatk2-prep":{
+   "repository":"arvados",
    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"picard-gatk2-prep",
    "script_parameters":{
@@ -71,9 +75,10 @@
    "runtime_constraints":{
     "max_tasks_per_node":1
    },
-   "output_is_persistent":false
+   "output_name":false
   },
   "GATK2-realign":{
+   "repository":"arvados",
    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"GATK2-realign",
    "script_parameters":{
@@ -102,9 +107,10 @@
    "runtime_constraints":{
     "max_tasks_per_node":2
    },
-   "output_is_persistent":false
+   "output_name":false
   },
   "GATK2-bqsr":{
+   "repository":"arvados",
    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"GATK2-bqsr",
    "script_parameters":{
@@ -124,9 +130,10 @@
      "required":true
     }
    },
-   "output_is_persistent":false
+   "output_name":false
   },
   "GATK2-merge-call":{
+   "repository":"arvados",
    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"GATK2-merge-call",
    "script_parameters":{
@@ -162,7 +169,7 @@
      ]
     }
    },
-   "output_is_persistent":true
+   "output_name":"Variant calls from UnifiedGenotyper"
   }
  }
 }