update portal workflow output for portal_cna_data_file to use merged …

…CNA file
mskcc · Apr 18, 2022 · a59bf42 · a59bf42
1 parent 40bbea8
commit a59bf42
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Showing 3 changed files with 5 additions and 18 deletions.
diff --git a/cwl/portal-workflow.cwl b/cwl/portal-workflow.cwl
@@ -498,7 +498,8 @@ outputs:
     outputSource: generate_meta_cna_segments/output_file  # <project_id>_meta_cna_hg19_seg.txt
   portal_cna_data_file:
     type: File
-    outputSource: clean_cna_headers/output_file # data_CNA.txt
+    # outputSource: clean_cna_headers/output_file # data_CNA.txt
+    outputSource: merge_cna/output_file # data_CNA.txt
   portal_cna_ascna_file:
     type: File
     outputSource: clean_ascna_headers/output_file # data_CNA.ascna.txt
@@ -514,9 +515,6 @@ outputs:
   portal_case_list_dir:
     type: Directory
     outputSource: make_case_list_dir/directory
-  merged_cna_file:
-    type: File
-    outputSource: merge_cna/output_file # data_CNA_merged.txt
   portal_report:
     type: File
     outputSource: compile_report/output_file
diff --git a/cwl/workflow_with_facets.cwl b/cwl/workflow_with_facets.cwl
@@ -402,7 +402,6 @@ steps:
       portal_hisens_segs, # <project_id>_data_cna_hg19.seg
       portal_fusions_data_file, # data_fusions.txt
       portal_case_list_dir,
-      merged_cna_file, # data_CNA_merged.txt -> data_CNA.txt
       portal_report
       ]
 
@@ -474,7 +473,7 @@ steps:
       portal_meta_fusions_file: run_portal_workflow/portal_meta_fusions_file # meta_fusions.txt
       portal_meta_mutations_extended_file: run_portal_workflow/portal_meta_mutations_extended_file # meta_mutations_extended.txt
       portal_meta_cna_segments_file: run_portal_workflow/portal_meta_cna_segments_file  # <project_id>_meta_cna_hg19_seg.txt
-      portal_cna_data_file: run_portal_workflow/merged_cna_file # data_CNA.txt ; replaces # portal_cna_data_file: run_portal_workflow/portal_cna_data_file # data_CNA.txt
+      portal_cna_data_file: run_portal_workflow/portal_cna_data_file # data_CNA.txt
       portal_cna_ascna_file: run_portal_workflow/portal_cna_ascna_file # data_CNA.ascna.txt
       portal_muts_file: merge_maf/output_file # data_mutations_extended.txt
       portal_hisens_segs: run_portal_workflow/portal_hisens_segs # # <project_id>_data_cna_hg19.seg

diff --git a/tests/test_portal-workflow_cwl.py b/tests/test_portal-workflow_cwl.py
@@ -85,8 +85,6 @@ def test_run_worflow_one_maf(self):
         output_json, output_dir = self.run_cwl()
 
         expected_output = {
-            'merged_cna_file': OFile(
-                name='data_CNA.txt', size=5355, hash='c1682f09406478fc404e40758b0c5e9c47dce5cb', dir = output_dir),
             'portal_case_list_dir': ODir(name='case_lists', items=[
                 OFile(name='cases_all.txt', size=604, hash='b8abebd686a5a4e3897af9546ee3e9e5fee8cf25'),
                 OFile(name='cases_cnaseq.txt', size=684, hash='3bc39070fa15b305c9b1f4a041b75c6a0ddbba9a'),
@@ -152,7 +150,7 @@ def test_run_worflow_one_maf(self):
         self.assertEqual(header_parts, expected_header_parts)
 
         # Test that CNA file looks correct
-        output_file = expected_output['merged_cna_file']['path']
+        output_file = expected_output['portal_cna_data_file']['path']
         lines = self.read_table(output_file)
         self.assertEqual(lines[0], ['Hugo_Symbol', 'Sample1'])
         self.assertEqual(len(lines), 587)
@@ -239,8 +237,6 @@ def test_run_worflow_two_mafs(self):
         output_json, output_dir = self.run_cwl()
 
         expected_output = {
-            'merged_cna_file': OFile(
-                name='data_CNA.txt', size=6764, hash='dd0e1181f412ddb30b4de4738f5b737e18a552be', dir=output_dir),
             'portal_case_list_dir': ODir(name='case_lists', items=[
                 OFile(name='cases_all.txt', size=604, hash='b8abebd686a5a4e3897af9546ee3e9e5fee8cf25'),
                 OFile(name='cases_cnaseq.txt', size=684, hash='3bc39070fa15b305c9b1f4a041b75c6a0ddbba9a'),
@@ -397,8 +393,6 @@ def test_with_facets_txt(self):
         output_json, output_dir = self.run_cwl()
 
         expected_output = {
-            'merged_cna_file': OFile(
-                name='data_CNA.txt', size=6398, hash='b25e5d8ed7cf067448e96db712de542df8d564cd', dir=output_dir),
             'portal_case_list_dir':
                 ODir(name='case_lists', items=[
                 OFile(name='cases_all.txt', size=194, hash='744b6aca3004f89bdb3f437ea87d4e3991394eaa'),
@@ -585,8 +579,6 @@ def test_with_facets_txt_and_facets_mafs(self):
         output_json, output_dir = self.run_cwl()
 
         expected_output = {
-            'merged_cna_file': OFile(
-                name='data_CNA.txt', size=9919, hash='ca32a20d522a1ab38816a800608a44b836ca96bf', dir=output_dir),
             'portal_case_list_dir': ODir(name='case_lists', items=[
                 OFile(name='cases_all.txt', size=194, hash='744b6aca3004f89bdb3f437ea87d4e3991394eaa'),
                 OFile(name='cases_cnaseq.txt', size=274, hash='9f7b03a5d0a9b8911c5c76ed0e6fe7712ee2a21f'),
@@ -597,7 +589,7 @@ def test_with_facets_txt_and_facets_mafs(self):
             'portal_cna_ascna_file': OFile(
                 name='data_CNA.ascna.txt', size=8593, hash='b322943e957285327f68c7d6033032af07a47c65', dir=output_dir),
             'portal_cna_data_file': OFile(
-                name='data_CNA.txt', size=6398, hash='b25e5d8ed7cf067448e96db712de542df8d564cd', dir=output_dir),
+                name='data_CNA.txt', size=9919, hash='ca32a20d522a1ab38816a800608a44b836ca96bf', dir=output_dir),
             'portal_data_clinical_patient_file': OFile(
                 name='data_clinical_patient.txt', size=91, hash='e45f9904b4de2c75fd148798075af9f05848aa27', dir=output_dir),
             'portal_data_clinical_sample_file': OFile(
@@ -758,8 +750,6 @@ def test_with_mixed_mafs(self):
         output_json, output_dir = self.run_cwl()
 
         expected_output = {
-            'merged_cna_file': OFile(
-                name='data_CNA.txt', size=6398, hash='b25e5d8ed7cf067448e96db712de542df8d564cd', dir=output_dir),
             'portal_case_list_dir': ODir(name='case_lists', items=[
                 OFile(name='cases_all.txt', size=194, hash='744b6aca3004f89bdb3f437ea87d4e3991394eaa'),
                 OFile(name='cases_cnaseq.txt', size=274, hash='9f7b03a5d0a9b8911c5c76ed0e6fe7712ee2a21f'),