From 01bd2cbbcf9f4ff1b998263edb95b87bbc7d471d Mon Sep 17 00:00:00 2001 From: Allan Bolipata Date: Wed, 18 Aug 2021 08:01:32 -0700 Subject: [PATCH] Fixed sample mapping output generator for argos 1.1.3 --- runner/operator/argos_operator/v1_1_3/argos_operator.py | 4 +--- 1 file changed, 1 insertion(+), 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 index 9c6b13923..51b51064a 100644 --- 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'])