From 9cd961c8b17be65f0360259a06989171cae115ae Mon Sep 17 00:00:00 2001 From: luc Date: Fri, 12 Apr 2024 09:09:32 -0400 Subject: [PATCH] fixed arc cmd option issue --- scripts/cellranger.py | 2 +- scripts/cellranger_config.py | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/scripts/cellranger.py b/scripts/cellranger.py index d5ed8fa..d238edd 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) + CONFIG.OPTIONS + cmd = "{}--id=Sample_{}{}".format(tool, sample, transcriptome) + "--libraries={}Sample_{}.csv".format(work_area, sample) + CONFIG.ARC_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) diff --git a/scripts/cellranger_config.py b/scripts/cellranger_config.py index 0d4a590..235488f 100644 --- a/scripts/cellranger_config.py +++ b/scripts/cellranger_config.py @@ -59,6 +59,7 @@ # cellranger command line options OPTIONS = " --create-bam=true --nopreflight --jobmode=lsf --mempercore=64 --disable-ui --maxjobs=200" +ARC_OPTIONS = " --nopreflight --jobmode=lsf --mempercore=64 --disable-ui --maxjobs=200" # 10X recipe list for different pipelines COUNT_FLAVORS = ["10X_Genomics_GeneExpression-3", "10X_Genomics_GeneExpression-5"]