diff --git a/scripts/cellranger.py b/scripts/cellranger.py index 5c5149e..d5ed8fa 100644 --- 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)