Update cellranger.py

mskcc · Feb 29, 2024 · 2fa413c · 2fa413c
1 parent f7e4d15
commit 2fa413c
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/scripts/cellranger.py b/scripts/cellranger.py
@@ -426,6 +426,10 @@ def lanuch_by_project(project_directory, recipe, species):
                     probe = config_dict[tag]["probe"][species]
                     cmd = cmd + " --probe-set={}".format(probe)
 
+                # if there is manual alignment json file availabe, add that to the cmd
+                if sample_info.json != "EMPTY":
+                    cmd = cmd + " --loupe-alignment={}".format(sample_info.json)
+
                 bsub_cmd = "bsub -J {}_{}_{}_SPATIAL -o {}_SPATIAL.out{}{}".format(sequencer_and_run, project, sample, sample, cmd, OPTIONS)
                 print(bsub_cmd)
                 subprocess.run(bsub_cmd, shell=True)