Merge pull request #918 from mskcc/bugfix/argos_operator

Fixed sample mapping output generator for argos operator 1.1.3
mskcc · Aug 19, 2021 · 497ddfd · 497ddfd
2 parents f9c5ddc + 01bd2cb
commit 497ddfd
Showing 1 changed file with 1 addition and 3 deletions.
diff --git a/runner/operator/argos_operator/v1_1_3/argos_operator.py b/runner/operator/argos_operator/v1_1_3/argos_operator.py
@@ -117,7 +117,7 @@ def get_jobs(self):
                     files.append(filepath)
             for p in job['pair'][0]['bam']:
                 filepath = FileProcessor.parse_path_from_uri(p['location'])
-                file_str = "\t".join([normal_sample_name, filepath]) + "\n"
+                file_str = "\t".join([tumor_sample_name, filepath]) + "\n"
                 if file_str not in check_for_duplicates:
                     check_for_duplicates.append(file_str)
                     sample_mapping += file_str
@@ -140,8 +140,6 @@ def get_jobs(self):
                     check_for_duplicates.append(file_str)
                     sample_mapping += file_str
                 if filepath not in files:
-                    sample_mapping += "\t".join(
-                        [normal_sample_name, filepath]) + "\n"
                     files.append(filepath)
             for p in job['pair'][1]['zR1']:
                 filepath = FileProcessor.parse_path_from_uri(p['location'])