Add monitor script for cellranger and update cromwell-metadata image (#…

…99) * Update monitor scripts and adapter docker tags. * Update the cromwell-metadata docker file. * Increase the cromwell-metadata docker image tag.
HumanCellAtlas · Oct 26, 2018 · 1708dc7 · 1708dc7
1 parent f20e5dc
commit 1708dc7
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Showing 8 changed files with 8 additions and 7 deletions.
diff --git a/adapter_pipelines/Optimus/adapter.wdl b/adapter_pipelines/Optimus/adapter.wdl
@@ -127,7 +127,7 @@ workflow AdapterOptimus {
   Int max_cromwell_retries = 0
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.39.0"
+  String pipeline_tools_version = "v0.40.0"
 
   call GetInputs as prep {
     input:

diff --git a/adapter_pipelines/Optimus/options.json b/adapter_pipelines/Optimus/options.json
@@ -1,4 +1,4 @@
 {
-  "monitoring_script": "gs://hca-dcp-mint-test-data/accessories/monitoring/optimus/monitor.sh",
+  "monitoring_script": "gs://hca-dcp-mint-test-data/accessories/monitoring/optimus/monitoring.sh",
   "read_from_cache": true
 }
diff --git a/adapter_pipelines/cellranger/adapter.wdl b/adapter_pipelines/cellranger/adapter.wdl
@@ -151,7 +151,7 @@ workflow Adapter10xCount {
   Int max_cromwell_retries = 0
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.39.0"
+  String pipeline_tools_version = "v0.40.0"
 
   call GetInputs {
     input:

diff --git a/adapter_pipelines/cellranger/options.json b/adapter_pipelines/cellranger/options.json
@@ -1,3 +1,4 @@
 {
+  "monitoring_script": "gs://hca-dcp-mint-test-data/accessories/monitoring/cellranger/monitoring.sh",
   "read_from_cache": true
 }
diff --git a/adapter_pipelines/ss2_single_sample/adapter.wdl b/adapter_pipelines/ss2_single_sample/adapter.wdl
@@ -83,7 +83,7 @@ workflow AdapterSmartSeq2SingleCell{
   Int max_cromwell_retries = 0
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.39.0"
+  String pipeline_tools_version = "v0.40.0"
 
   call GetInputs as prep {
     input:

diff --git a/adapter_pipelines/ss2_single_sample/options.json b/adapter_pipelines/ss2_single_sample/options.json
@@ -1,4 +1,4 @@
 {
-  "monitoring_script": "gs://hca-dcp-mint-test-data/accessories/monitoring/smartseq2/monitor.sh",
+  "monitoring_script": "gs://hca-dcp-mint-test-data/accessories/monitoring/smartseq2/monitoring.sh",
   "read_from_cache": true
 }
diff --git a/adapter_pipelines/submit.wdl b/adapter_pipelines/submit.wdl
@@ -29,7 +29,7 @@ task get_metadata {
       --use_caas ${use_caas}
   >>>
   runtime {
-    docker: (if runtime_environment == "production" then "gcr.io/hca-dcp-pipelines-prod/cromwell-metadata:" else "gcr.io/broad-dsde-mint-${runtime_environment}/cromwell-metadata:") + "v1.1.0"
+    docker: (if runtime_environment == "production" then "gcr.io/hca-dcp-pipelines-prod/cromwell-metadata:" else "gcr.io/broad-dsde-mint-${runtime_environment}/cromwell-metadata:") + "v1.2.0"
     maxRetries: max_retries
   }
   output {

diff --git a/docker/cromwell-metadata/Dockerfile b/docker/cromwell-metadata/Dockerfile
@@ -1,4 +1,4 @@
-FROM quay.io/humancellatlas/secondary-analysis-pipeline-tools:v0.29.0
+FROM quay.io/humancellatlas/secondary-analysis-pipeline-tools:v0.40.0
 
 RUN mkdir /cromwell-metadata
 WORKDIR /cromwell-metadata