From 4e7eeb94a4c6f920fe7ebfc9b8dc0ea582a7f878 Mon Sep 17 00:00:00 2001 From: luc Date: Fri, 9 Aug 2024 10:17:40 -0400 Subject: [PATCH] Update cellranger_multi.py --- scripts/cellranger_multi.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/scripts/cellranger_multi.py b/scripts/cellranger_multi.py index 78b2827..17bf943 100644 --- a/scripts/cellranger_multi.py +++ b/scripts/cellranger_multi.py @@ -87,7 +87,8 @@ def write_to_csv(self, name_of_file): file.write("[gene-expression]\n") for key, value in self.gene_expression.items(): file.write("{},{}\n".format(key, value)) - + file.write("create-bam,true\n") + file.write("\n[libraries]\nfastq_id,fastqs,feature_types\n") for key, value in self.lirbaries.items(): @@ -110,7 +111,8 @@ def write_ch_ge_only_to_csv(self, name_of_file): file.write("[gene-expression]\n") for key, value in self.gene_expression.items(): file.write("{},{}\n".format(key, value)) - + file.write("create-bam,true\n") + file.write("\n[libraries]\nfastq_id,fastqs,feature_types\n") for key, value in self.lirbaries.items(): @@ -131,6 +133,7 @@ def new_config_and_generate_cmd(self): file.write("[gene-expression]\n") file.write("{},{}\n".format("reference", self.gene_expression["reference"])) file.write("force-cells, {}\ncheck-library-compatibility,FALSE\n".format(value[0])) + file.write("create-bam,true\n") file.write("\n[libraries]\nfastq_id,fastqs,feature_types\n")