Consolidate ome-tiff-pyramid DAGs

.gitmodules

@@ -31,6 +31,3 @@
 [submodule "src/ingest-pipeline/airflow/dags/cwl/sn-atac-seq-pipeline"]
 	path = src/ingest-pipeline/airflow/dags/cwl/sn-atac-seq-pipeline
 	url = https://github.com/hubmapconsortium/sc-atac-seq-pipeline
-[submodule "src/ingest-pipeline/airflow/dags/cwl/ome-tiff-pyramid-ims"]
-	path = src/ingest-pipeline/airflow/dags/cwl/ome-tiff-pyramid-ims
-	url = https://github.com/hubmapconsortium/ome-tiff-pyramid

src/ingest-pipeline/airflow/dags/ometiff_pyramid.py

@@ -34,6 +34,9 @@
     localized_assert_json_matches_schema as assert_json_matches_schema,
 )
 
+# Passed directly to the pipeline
+DOWNSAMPLE_TYPE = 'LINEAR'
+
 # after running this DAG you should have on disk
 # 1. 1 OME.TIFF pyramid per OME.TIFF in the original dataset
 # 2. 1 .N5 file per OME.TIFF in the original dataset
@@ -93,13 +96,19 @@ def build_cwltool_cmd1(**kwargs):
         data_dir = ctx['parent_lz_path']
         print('data_dir: ', data_dir)
 
+        # TODO: implement this check however is appropriate
+        is_ims = False
+
         #this is the call to the CWL
         command = [
             *get_cwltool_base_cmd(tmpdir),
             cwl_workflows[0],
             '--ometiff_directory',
             data_dir,
         ]
+        if is_ims:
+            command.append('--downsample_type')
+            command.append(DOWNSAMPLE_TYPE)
 
         return join_quote_command_str(command)