Fix/atera

src/base/labels_nebius.config

@@ -132,6 +132,17 @@ process {
     containerOptions = { workflow.containerEngine == "singularity" ? '--nv':
        ( workflow.containerEngine == "docker" ? '--gpus all': null ) }
   }
+  withLabel: gpuh100 {
+    // Nebius H100 gpu-node-group: NVIDIA H100 SXM, 1 GPU, 16 CPUs, 196 GiB RAM
+    // ~195 GiB / ~15.9 vCPU allocatable — cap well below node max to leave headroom
+    cpus = 12
+    accelerator = 1
+    memory = { [ 120.GB * task.attempt, 180.GB ].min() }
+    disk = 200.GB
+    pod = [[nodeSelector: 'nebius.com/node-group-id=mk8snodegroup-e00jp7hyqr094tmy35']]
+    containerOptions = { workflow.containerEngine == "singularity" ? '--nv':
+       ( workflow.containerEngine == "docker" ? '--gpus all': null ) }
+  }
 
 withLabel: hightime    { time = 12.h }
 withLabel: veryhightime { time = 24.h }

src/methods_calculate_cell_volume/alpha_shapes/script.py

@@ -15,7 +15,7 @@
 sdata = sd.read_zarr(par['input'])
 
 print('Determine cell ids', flush=True)
-cell_ids = sorted(sdata["transcripts"]["cell_id"].unique())
+cell_ids = sorted(sdata["transcripts"]["cell_id"].unique().compute())
 if cell_ids[0] == 0:
     cell_ids = cell_ids[1:]
 

src/methods_cell_type_annotation/moscot/config.vsh.yaml

@@ -57,4 +57,4 @@ runners:
   - type: executable
   - type: nextflow
     directives:
-      label: [ hightime, midcpu, veryhighmem, gpuhighmem ]
+      label: [ hightime, midcpu, veryhighmem, gpuh100 ]

src/methods_cell_type_annotation/tangram/config.vsh.yaml

@@ -40,4 +40,4 @@ runners:
   - type: executable
   - type: nextflow
     directives:
-      label: [ midtime, midcpu, midmem, gpuhighmem ]
+      label: [ midtime, midcpu, midmem, gpuh100 ]