From 051e30b133b443e1b5f690bc8c7aa4240ddc9c3a Mon Sep 17 00:00:00 2001 From: luc Date: Wed, 17 Apr 2024 15:17:38 -0400 Subject: [PATCH] Update cellranger_multi.py --- scripts/cellranger_multi.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/scripts/cellranger_multi.py b/scripts/cellranger_multi.py index 47f9b1d..47838b4 100644 --- a/scripts/cellranger_multi.py +++ b/scripts/cellranger_multi.py @@ -114,6 +114,7 @@ def write_ch_ge_only_to_csv(self, name_of_file): file.write("\n[libraries]\nfastq_id,fastqs,feature_types\n") for key, value in self.lirbaries.items(): + key.replace("_CHMARKER_", "") if value[1] == "Gene Expression" or value[1] == "Multiplexing Capture": for i in value[0]: file.write("{},{},{}\n".format(key, i, value[1])) @@ -252,7 +253,11 @@ def gather_config_info(sample_dict, genome, IGO_ID): elif key == "fb": config.lirbaries[value] = [fastq_list[value], "Antibody Capture"] elif key == "ch": - config.lirbaries[value] = [fastq_list[value], "Multiplexing Capture"] + # for case of all ch, fb and vdj exits and doesn't need to make two copies of fb fastq file + if "ch" in sample_dict.keys() and "fb" in sample_dict.keys() and "vdj" in sample_dict.keys(): + config.lirbaries[value + "_CHMARKER_"] = [fastq_list[value], "Multiplexing Capture"] + else: + config.lirbaries[value] = [fastq_list[value], "Multiplexing Capture"] return config