Atera

src/base/labels_nebius.config

@@ -74,7 +74,7 @@ process {
     // Nebius gpu-node-group: NVIDIA L40S, 1 GPU, 8 CPUs, 32 GiB RAM
     cpus = 6
     accelerator = 1
-    memory = 26.GB
+    memory = 100.GB
     disk = 200.GB
     pod = [[nodeSelector: 'nebius.com/node-group-id=mk8snodegroup-e00t775jb99svb7k5r']]
     containerOptions = { workflow.containerEngine == "singularity" ? '--nv':

src/datasets/loaders/tenx_atera/script.py

@@ -42,7 +42,12 @@
         print(f"Extracting input zip to {tmpdirname}", flush=True)
         with zipfile.ZipFile(par_input, "r") as zip_ref:
             zip_ref.extractall(tmpdirname)
-            par_input = tmpdirname
+        # find the directory containing the Xenium output files (may be nested)
+        par_input = tmpdirname
+        for root, dirs, files in os.walk(tmpdirname):
+            if "cell_feature_matrix.h5" in files:
+                par_input = root
+                break
 
     # read the data
     sdata = xenium(

src/datasets/loaders/tenx_xenium/script.py

@@ -42,7 +42,12 @@
         print(f"Extracting input zip to {tmpdirname}", flush=True)
         with zipfile.ZipFile(par_input, "r") as zip_ref:
             zip_ref.extractall(tmpdirname)
-            par_input = tmpdirname
+        # find the directory containing the Xenium output files (may be nested)
+        par_input = tmpdirname
+        for root, dirs, files in os.walk(tmpdirname):
+            if "cell_feature_matrix.h5" in files:
+                par_input = root
+                break
 
     # read the data
     sdata = xenium(