From 0103c746f8b61e692281d639baa27dca6f503390 Mon Sep 17 00:00:00 2001 From: luc Date: Thu, 29 Aug 2024 14:27:56 -0400 Subject: [PATCH] update cellranger parameter --- scripts/cellranger_config.py | 4 ++-- scripts/cellranger_multi.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/scripts/cellranger_config.py b/scripts/cellranger_config.py index 043fba3..f948b28 100644 --- 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 index 568a62c..3d95f8c 100644 --- 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: