np hca adapter test (#372)

* add test for hca adapter

* fix test inputs json and add http imports for testing

* switch inputs

* update cromwell url

* change to relative imports

* update test inputs to dev/null

* update test inputs

* change to http imports for terra testing

* update ValidateHcaAdapter.wdl for testing

* update ValidateHcaAdapter.wdl for testing

* update ValidateHcaAdapter.wdl for testing

* update ValidateHcaAdapter.wdl for testing

* fix task

* revert everything

* testing

* zcat to cat

* update ValidateOptimusDescriptorAnalysisFiles

* testing

* testing

* revert everything again

* testing

* testing

* testing

* update ValidateOptimusDescriptorAnalysisFiles

* update ValidateOptimusDescriptorAnalysisFiles

* update ValidateOptimusDescriptorAnalysisFiles

* update ValidateOptimusDescriptorAnalysisFiles

* update ValidateOptimusDescriptorAnalysisFiles

* update ValidateOptimusLinksFiles

* update ValidateOptimusLinksFiles

* adding more tasks

* fix hashes

* fix hashes

* try diff for links json

* try diff for links json

* try diff for links json

* testing

* testing

* remove optimus

* fix inputs

* fix hashes

* fix hashes

* change all tasks to use diff

* switch indices

* switch indices

* testing

* testing

* more testing

* more testing

* adding in ss2 truth inputs and calls/tasks

* fix ss2_metadata_analysis_file_intermediate_bai_json_truth

* adding in more ss2 related tasks, adding in more outputs to getTerraMetadata.wdl

* fix typo

* change to http import so terra understands

* rename input to OptimusPostProcessing.wdl

* rename library input to OptimusPostProcessing.wdl

* rename library input to OptimusPostProcessing.wdl

* undo

* undo

* testing

* add validation for optimus post processing

* undo some validation

* add links validation

* add ValidateOptimusMetadataProjectLevelAnalysisFiles validation

* add ValidateOptimusMetadataProjectLevelAnalysisProcess validation

* add ValidateOptimusMetadataProjectLevelAnalysisProtocol validation

* clean up ss2 from optimus_test_hca_adapter_PR.wdl

* clean up some text in ValidateHcaAdapter.wdl

* update optimus imports back to relative

* updating test wdl to match whats in terra

* remove test inputs json

* collapse all tasks into one task

* type

* another weird type

* collapsing tasks into 1, moving get terra metadata wdl

* fix import

* change to relative imports, add test wdl to dockstore

* whiteespace

Co-authored-by: jessicaway <jway@broadinstitute.org>

Author: nikellepetrillo

.dockstore.yml

@@ -47,4 +47,8 @@ workflows:
 
   - name: CEMBA
     subclass: WDL
-    primaryDescriptorPath: /pipelines/cemba/cemba_methylcseq/CEMBA.wdl
+    primaryDescriptorPath: /pipelines/cemba/cemba_methylcseq/CEMBA.wdl
+
+  - name: OptimusTestHcaAdapter
+    subclass: WDL
+    primaryDescriptorPath: /tests/skylab/hca_adapter/pr/optimus_test_hca_adapter_PR.wdl

projects/hca_mvp/OptimusPostProcessing.wdl

@@ -12,36 +12,36 @@ workflow OptimusPostProcessing {
     Array[File] library_looms
     Array[File] analysis_file_jsons
     Array[File] links_jsons
-    Array[String] library
+    Array[String] post_processing_library
     Array[String] species
     Array[String] organ
     String project_id
     String project_name
     String output_basename
-    String staging_area = "gs://broad-dsp-monster-hca-prod-lantern/"
+    String post_processing_staging_area = "gs://broad-dsp-monster-hca-prod-lantern/"
     String version_timestamp = "2021-05-24T12:00:00.000000Z"
   }
 
 
   # version of this pipeline
   String pipeline_version = "1.0.0"
 
-  String project_stratum_string = "project=" + project_id + ";library=" + library[0] + ";species=" + species[0] + ";organ=" + organ[0]
+  String project_stratum_string = "project=" + project_id + ";library=" + post_processing_library[0] + ";species=" + species[0] + ";organ=" + organ[0]
 
   # Build staging bucket
-  String staging_bucket = staging_area + project_id + "/staging/"
+  String staging_bucket = post_processing_staging_area + project_id + "/staging/"
 
   call PostProcessing.CheckMetadata {
       input:
-        library = library,
+        library = post_processing_library,
         species = species,
         organ = organ
   }
 
   call PostProcessing.MergeLooms {
     input:
       library_looms = library_looms,
-      library = library[0],
+      library = post_processing_library[0],
       species = species[0],
       organ = organ[0],
       project_id = project_id,