From a59bf42c0fea3e2a788aa5eadd9e7ca5c583cc44 Mon Sep 17 00:00:00 2001 From: Stephen Kelly Date: Mon, 18 Apr 2022 12:18:09 -0400 Subject: [PATCH] update portal workflow output for portal_cna_data_file to use merged CNA file --- cwl/portal-workflow.cwl | 6 ++---- cwl/workflow_with_facets.cwl | 3 +-- tests/test_portal-workflow_cwl.py | 14 ++------------ 3 files changed, 5 insertions(+), 18 deletions(-) diff --git a/cwl/portal-workflow.cwl b/cwl/portal-workflow.cwl index 9e4d861..7171070 100644 --- a/cwl/portal-workflow.cwl +++ b/cwl/portal-workflow.cwl @@ -498,7 +498,8 @@ outputs: outputSource: generate_meta_cna_segments/output_file # _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 index def48f8..04f1950 100644 --- a/cwl/workflow_with_facets.cwl +++ b/cwl/workflow_with_facets.cwl @@ -402,7 +402,6 @@ steps: portal_hisens_segs, # _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 # _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 # # _data_cna_hg19.seg diff --git a/tests/test_portal-workflow_cwl.py b/tests/test_portal-workflow_cwl.py index 9185380..09cd7b3 100755 --- 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'),