update cellranger parameter

mskcc · Aug 29, 2024 · 0103c74 · 0103c74
1 parent 10a1271
commit 0103c74
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/scripts/cellranger_config.py b/scripts/cellranger_config.py
@@ -53,10 +53,10 @@
 ARC_FLAVORS = ["SC_Chromium-Multiome", "SC_Chromium-Multiome-ATAC", "SC_Chromium-Multiome-GEX"]
 SPATIAL_FLAVORS = ["ST_Visium", "ST_Visium-HD"]
 
-# we do not want to PROCESS SAIL (15500) or SCRI (12437) projects
+# we do not want to PROCESS SAIL (15500) or SCRI (12437) projects, adding new chemistry for SAIL, 16364
 SCRI = "12437"
 SAIL = "15500"
-DO_NOT_PROCESS = [SCRI, SAIL]
+DO_NOT_PROCESS = [SCRI, SAIL, "16364"]
 
 VISIUM_ENDPOINT = "https://igolims.mskcc.org:8443/LimsRest/getConfig?igoId="
 original_tiff_images_directory = "/rtssdc/mohibullahlab/IGO_Pipeline_Results/Single_Cell/10X_Genomics/TIFF_Images/"

diff --git a/scripts/cellranger_multi.py b/scripts/cellranger_multi.py
@@ -441,7 +441,7 @@ def gather_sample_set_info(sample_name):
     # using ilab and sample name for this 
     for sample in response_data:
         for key, value in sample.items():
-            if value[0].startswith(ilab_request) and key.endswith(sample_number):
+            if value[0].startswith(ilab_request[:-1]) and key.endswith(sample_number):
                 value[2] = value[2].split(",")
                 if "SC_Chromium-FB-5" in value[2][0] or "SC_Chromium-FB-3" in value[2][0]:
                     if "Feature Barcoding" in fb_type: