fixed arc cmd option issue

mskcc · Apr 12, 2024 · 9cd961c · 9cd961c
1 parent 189c214
commit 9cd961c
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Showing 2 changed files with 2 additions 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) + 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
@@ -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"]