Fix submission wdl (#157)

* Fix confirm-submission task Add runtime_environment to confirm submission task inputs and pass it to the script along with the service account key. * Change pipeline-tools version for testing * Fix image name * Fix errors * Update pipeline-tools version
HumanCellAtlas · Jul 5, 2019 · 92f4983 · 92f4983
1 parent 323eb91
commit 92f4983
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Showing 7 changed files with 9 additions and 6 deletions.
diff --git a/adapter_pipelines/Optimus/adapter.wdl b/adapter_pipelines/Optimus/adapter.wdl
@@ -139,7 +139,7 @@ workflow AdapterOptimus {
   Int max_cromwell_retries = 0
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.54.0"
+  String pipeline_tools_version = "v0.54.1"
 
   call GetInputs as prep {
     input:

diff --git a/adapter_pipelines/cellranger/adapter.wdl b/adapter_pipelines/cellranger/adapter.wdl
@@ -149,7 +149,7 @@ workflow Adapter10xCount {
   Int max_cromwell_retries = 0
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.54.0"
+  String pipeline_tools_version = "v0.54.1"
 
   call GetInputs {
     input:

diff --git a/adapter_pipelines/ss2_single_end/adapter.wdl b/adapter_pipelines/ss2_single_end/adapter.wdl
@@ -70,7 +70,7 @@ workflow AdapterSmartSeq2SingleCellUnpaired {
   Int max_cromwell_retries = 0
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.54.0"
+  String pipeline_tools_version = "v0.54.1"
 
   call GetInputs as prep {
     input:

diff --git a/adapter_pipelines/ss2_single_sample/adapter.wdl b/adapter_pipelines/ss2_single_sample/adapter.wdl
@@ -70,7 +70,7 @@ workflow AdapterSmartSeq2SingleCell{
   Int max_cromwell_retries = 0
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.54.0"
+  String pipeline_tools_version = "v0.54.1"
 
   call GetInputs as prep {
     input:

diff --git a/adapter_pipelines/submit.wdl b/adapter_pipelines/submit.wdl
@@ -205,6 +205,7 @@ task confirm_submission {
   Int? individual_request_timeout
   Boolean record_http
   String pipeline_tools_version
+  String runtime_environment
   File service_account_key_path
 
   command <<<
@@ -221,7 +222,9 @@ task confirm_submission {
     export PYTHONUNBUFFERED=TRUE
 
     # Confirm the submission
-    confirm-submission --envelope_url ${submission_url}
+    confirm-submission --envelope_url ${submission_url} \
+      --runtime_environment ${runtime_environment} \
+      --service_account_key_path ${service_account_key_path}
   >>>
 
   runtime {

diff --git a/adapter_pipelines/submit_stub/submit.wdl b/adapter_pipelines/submit_stub/submit.wdl
@@ -36,6 +36,7 @@ workflow submit {
   String pipeline_version
   # Disk space to allocate for stage_files task
   Int disk_space
+  File service_account_key_path = "gs://broad-dsde-mint-${runtime_environment}-credentials/caas_key.json"
 
   call submit_stub
 

diff --git a/pipeline_tools/shared/submission/create_envelope.py b/pipeline_tools/shared/submission/create_envelope.py
@@ -409,7 +409,6 @@ def link_analysis_protocol_to_analysis_process(
     response = http_requests.put(
         link_url, headers=link_headers, data=analysis_protocol_url
     )
-    return response.json()
 
 
 def main():