bug fix

mskcc · Nov 24, 2023 · 75709bc · 75709bc
1 parent b1ab663
commit 75709bc
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/scripts/cellranger.py b/scripts/cellranger.py
@@ -68,7 +68,7 @@
         "tool": " /igo/work/nabors/tools/spaceranger-2.0.0/spaceranger count ",
         "genome": {
             "Human": " --transcriptome=/igo/work/nabors/genomes/10X_Genomics/GEX/refdata-gex-GRCh38-2020-A ",
-            "Mouse": " --transcriptome=/igo/work/nabors/genomes/10X_Genomics/spatial_gex/refdata-gex-mm10-2020-A"
+            "Mouse": " --transcriptome=/igo/work/nabors/genomes/10X_Genomics/spatial_gex/refdata-gex-mm10-2020-A "
         },
         "probe": {
             "Human": "/igo/work/nabors/genomes/10X_Genomics/spatial_gex/Visium_Human_Transcriptome_Probe_Set_v1.0_GRCh38-2020-A.csv",

diff --git a/scripts/cellranger_multi.py b/scripts/cellranger_multi.py
@@ -197,9 +197,10 @@ def ch_file_generation(project_id, sample_name):
 
     # write ch config file for this sample
     file_name = "{}Project_{}/Project_{}_ch_{}.csv".format(CONFIG_AREA, project_id, project_id, sample_name)
-    if not os.path.exists(os.path.dirname(file_name)):
+    try:
         os.makedirs(os.path.dirname(file_name))
-
+    except OSError as error:
+        print(error) 
     with open(file_name,'w') as file:
         file.write("id,name,read,pattern,sequence,feature_type\n")
         for tag in sub_sample_dict.values():