X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/64b24877bdb4b35938e8b691463b78073a4fd31d..bdb591e730fffb6aba7c01d93528c59da91b05b0:/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 f84ad3fb52..f8c08d146a 100644
--- 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
   },
   "bwa-index":{
+   "repository":"arvados",
    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"bwa-index",
    "script_parameters":{
@@ -29,6 +31,7 @@
    "output_is_persistent":false
   },
   "bwa-aln":{
+   "repository":"arvados",
    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"bwa-aln",
    "script_parameters":{
@@ -54,6 +57,7 @@
    "output_is_persistent":false
   },
   "picard-gatk2-prep":{
+   "repository":"arvados",
    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"picard-gatk2-prep",
    "script_parameters":{
@@ -74,6 +78,7 @@
    "output_is_persistent":false
   },
   "GATK2-realign":{
+   "repository":"arvados",
    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"GATK2-realign",
    "script_parameters":{
@@ -105,6 +110,7 @@
    "output_is_persistent":false
   },
   "GATK2-bqsr":{
+   "repository":"arvados",
    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"GATK2-bqsr",
    "script_parameters":{
@@ -127,6 +133,7 @@
    "output_is_persistent":false
   },
   "GATK2-merge-call":{
+   "repository":"arvados",
    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"GATK2-merge-call",
    "script_parameters":{