Update cellranger_multi.py

mskcc · Aug 9, 2024 · 4e7eeb9 · 4e7eeb9
1 parent d544d1f
commit 4e7eeb9
Showing 1 changed file with 5 additions and 2 deletions.
diff --git 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")