Update cellranger.py

mskcc · Apr 1, 2024 · a1ab25e · a1ab25e
1 parent 85dd231
commit a1ab25e
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/scripts/cellranger.py b/scripts/cellranger.py
@@ -173,7 +173,7 @@ def lanuch_by_project(sequencer_and_run, project, sample_id_list, sample_genome_
                 create_library_csv_file(validation[1], validation[2], sample)
                 tool = CONFIG.config_dict[tag]["tool"]
                 transcriptome = CONFIG.config_dict[tag]["genome"][sample_genome_dict[sample]]
-                cmd = "{}--id=Sample_{}{}".format(tool, sample, transcriptome) + "--libraries={}Sample_{}.csv".format(work_area, sample) + OPTIONS
+                cmd = "{}--id=Sample_{}{}".format(tool, sample, transcriptome) + "--libraries={}Sample_{}.csv".format(work_area, sample) + CONFIG.OPTIONS
                 bsub_cmd = "bsub -J {}_{}_{}_ARC -o {}_ARC.out{}".format(sequencer_and_run, project, sample, sample, cmd)
                 print(bsub_cmd)
                 subprocess.run(bsub_cmd, shell=True)