updated run time of master process

Author: ctastad

cholab-prep/example_xenium-multichannel-config.yaml

@@ -55,10 +55,10 @@ segmentation:
         z: "z"
 
       segmentation:
-        scale: 10 # [important parameter] typical cell radius in microns
+        #scale: 10 # [important parameter] typical cell radius in microns
         scale_std: "25%" # cell radius standard deviation
         prior_segmentation_confidence: 1.0 # confidence of the cellpose confidence (float in [0, 1])
-        estimate_scale_from_centers: false
+        estimate_scale_from_centers: true
         n_clusters: 4
         iters: 500
         n_cells_init: 0
@@ -79,7 +79,7 @@ annotation:
   method: tangram
   args:
     sc_reference_path: /sc/arion/projects/untreatedIBD/cache/reference-objects/oliver-2024-subset.h5ad # path to the annotated scRNAseq reference used by Tangram
-    cell_type_key: level_2_annot # key of adata_ref.obs containing the cell-type annotation
+    cell_type_key: cell_type # key of adata_ref.obs containing the cell-type annotation
     reference_preprocessing: log1p # if your reference `adata.X` contains raw counts, then remove this parameter from the config. Else, choose "log1p" (if you have already run both `sc.pp.normalize_total` and `sc.pp.log1p` on your reference) or "normalized" (if you have already run `sc.pp.normalize_total` on your reference)
 
   # [only if you choose the simple staining-based annotation (comment out the lines below)]

cholab-prep/prep-sopa-run/src/lsf.py

@@ -37,9 +37,9 @@ def create_lsf_script(
 
     script_content = f"""#BSUB -J sopa-{sample_name}
 #BSUB -P acc_untreatedIBD
-#BSUB -W 8:00
+#BSUB -W 24:00
 #BSUB -q {queue}
-#BSUB -n 4
+#BSUB -n 2
 #BSUB -R span[hosts=1]
 #BSUB -R rusage[mem=4G]
 #BSUB -u {email}

workflow/lsf/config.yaml

@@ -12,7 +12,7 @@ cluster:
 default-resources:
   threads: 8
   time: 1:00
-  queue: express
+  queue: premium
   mem_mb: 16_000
 
 restart-times: 3