Increase rename files task disk space (#98)

* Increase rename files task disk space

* Fix submit WDL for production. (#97)

* Increase rename files task disk space

* Fix submit WDL for production.

* Update pipeline-tools version

Author: samanehsan

adapter_pipelines/Optimus/adapter.wdl

@@ -127,7 +127,7 @@ workflow AdapterOptimus {
   Int max_cromwell_retries = 0
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.38.0"
+  String pipeline_tools_version = "v0.39.0"
 
   call GetInputs as prep {
     input:

adapter_pipelines/cellranger/adapter.wdl

@@ -62,14 +62,15 @@ task RenameFiles {
     >>>
     runtime {
       docker: "quay.io/humancellatlas/secondary-analysis-pipeline-tools:" + pipeline_tools_version
+      disks: "local-disk 100 HDD"
     }
     output {
       Array[File] outputs = new_file_names
     }
 }
 
 task InputsForSubmit {
-    Array[File] fastqs
+    Array[String] fastqs
     Array[Object] other_inputs
     Int? expect_cells
     String pipeline_tools_version
@@ -150,7 +151,7 @@ workflow Adapter10xCount {
   Int max_cromwell_retries = 0
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.38.0"
+  String pipeline_tools_version = "v0.39.0"
 
   call GetInputs {
     input:

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 = "v0.38.0"
+  String pipeline_tools_version = "v0.39.0"
 
   call GetInputs as prep {
     input:

adapter_pipelines/submit.wdl

@@ -29,7 +29,7 @@ task get_metadata {
       --use_caas ${use_caas}
   >>>
   runtime {
-    docker: "gcr.io/broad-dsde-mint-${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:") + "v1.1.0"
     maxRetries: max_retries
   }
   output {