From 3365f10eef3b0afd560f30526aed2632216c0901 Mon Sep 17 00:00:00 2001
From: Stephen Kelly <stevekm@users.noreply.github.com>
Date: Tue, 31 Aug 2021 14:53:35 -0400
Subject: [PATCH] add extra CNA files to workflow with facets

---
 cwl/portal-workflow.cwl            |  2 +-
 cwl/workflow_with_facets.cwl       | 10 +++++++-
 tests/test_workflow_with_facets.py | 38 +++++++++++++++++++++++++++---
 3 files changed, 45 insertions(+), 5 deletions(-)

diff --git a/cwl/portal-workflow.cwl b/cwl/portal-workflow.cwl
index 18f3c65..50c1d54 100644
--- a/cwl/portal-workflow.cwl
+++ b/cwl/portal-workflow.cwl
@@ -150,7 +150,7 @@ inputs:
     - "null"
     - File
   extra_cna_files:
-    doc: "An extra CNA data file to be merged in with the portal CNA data"
+    doc: "Extra CNA data files to be merged in with the portal CNA data"
     type:
     - "null"
     - File[]
diff --git a/cwl/workflow_with_facets.cwl b/cwl/workflow_with_facets.cwl
index f17f3e9..c9a929c 100644
--- a/cwl/workflow_with_facets.cwl
+++ b/cwl/workflow_with_facets.cwl
@@ -281,6 +281,11 @@ inputs:
     doc: "Array of tumor bam files. Must match the same order of sample pairs in 'pairs' input field"
     secondaryFiles:
         - ^.bai
+  extra_cna_files:
+    doc: "Extra CNA data files to be merged in with the portal CNA data"
+    type:
+    - "null"
+    - File[]
 
 
 steps:
@@ -396,7 +401,8 @@ steps:
       portal_muts_file, # data_mutations_extended.txt
       portal_hisens_segs, # <project_id>_data_cna_hg19.seg
       portal_fusions_data_file, # data_fusions.txt
-      portal_case_list_dir
+      portal_case_list_dir,
+      merged_cna_file # data_CNA_merged.txt
       ]
 
   # need to merge the portal mutations maf with the Facets maf to get some extra information in the output
@@ -473,6 +479,7 @@ steps:
       portal_hisens_segs: run_portal_workflow/portal_hisens_segs # # <project_id>_data_cna_hg19.seg
       portal_fusions_data_file: run_portal_workflow/portal_fusions_data_file # data_fusions.txt
       portal_case_list_dir: run_portal_workflow/portal_case_list_dir
+      merged_cna_file: run_portal_workflow/merged_cna_file
       output_directory_name:
         valueFrom: ${ return "portal"; }
       files:
@@ -492,6 +499,7 @@ steps:
           inputs.portal_hisens_segs,
           inputs.portal_fusions_data_file,
           inputs.portal_case_list_dir,
+          inputs.merged_cna_file
           ]}
     out: [ directory ]
 
diff --git a/tests/test_workflow_with_facets.py b/tests/test_workflow_with_facets.py
index 738c081..30e4d88 100755
--- a/tests/test_workflow_with_facets.py
+++ b/tests/test_workflow_with_facets.py
@@ -369,6 +369,14 @@ def test_demo_dataset1(self):
                                 'size': 213,
                                 'path': os.path.join(output_dir, 'portal/case_lists/cases_sequenced.txt')}
                             ]
+                        },
+                        {
+                            'basename': 'data_CNA_merged.txt',
+                            'checksum': 'sha1$df07ff6b94392c470e2c8c47ca6e35cc2f6cc791',
+                            'class': 'File',
+                            'location': 'file://' + os.path.join(output_dir, 'portal/data_CNA_merged.txt'),
+                            'path': os.path.join(output_dir, 'portal/data_CNA_merged.txt'),
+                            'size': 2343
                         }
                     ]
                 }
@@ -878,7 +886,15 @@ def test_demo_dataset2(self):
                                 'size': 213,
                                 'path': os.path.join(output_dir, 'portal/case_lists/cases_sequenced.txt')}
                             ]
-                        }
+                        },
+                        {
+                            'basename': 'data_CNA_merged.txt',
+                            'checksum': 'sha1$ddc7acafdb61a3ea2aa1ec02e01df7bcc1691267',
+                            'class': 'File',
+                            'location': 'file://' + os.path.join(output_dir, 'portal/data_CNA_merged.txt'),
+                            'path': os.path.join(output_dir, 'portal/data_CNA_merged.txt'),
+                            'size': 3808
+                        },
                     ]
                 }
             }
@@ -1308,7 +1324,15 @@ def test_run_worflow_one_maf(self):
                                 'size': 641,
                                 'path': os.path.join(output_dir, 'portal/case_lists/cases_sequenced.txt')}
                             ]
-                        }
+                        },
+                        {
+                            'basename': 'data_CNA_merged.txt',
+                            'checksum': 'sha1$dca846b4f25ca20bca814fa15351de8d322d3439',
+                            'class': 'File',
+                            'location': 'file://' + os.path.join(output_dir, 'portal/data_CNA_merged.txt'),
+                            'path': os.path.join(output_dir, 'portal/data_CNA_merged.txt'),
+                            'size': 5319
+                        },
                     ]
                 }
             }
@@ -1792,7 +1816,15 @@ def test_run_worflow_two_mafs(self):
                     'size': 641,
                     'path': os.path.join(output_dir, 'portal/case_lists/cases_sequenced.txt')}],
                     'location': 'file://' + os.path.join(output_dir, 'portal/case_lists'),
-                    'path': os.path.join(output_dir, 'portal/case_lists')}
+                    'path': os.path.join(output_dir, 'portal/case_lists')},
+                    {
+                        'basename': 'data_CNA_merged.txt',
+                        'checksum': 'sha1$4795ba3d6c30a028d21bafbb55227ede294b61d5',
+                        'class': 'File',
+                        'location': 'file://' + os.path.join(output_dir, 'portal/data_CNA_merged.txt'),
+                        'path': os.path.join(output_dir, 'portal/data_CNA_merged.txt'),
+                        'size': 6727
+                    }
                 ]
             }
         }