Add gpu for moscot and change parallelization of baysor (#56)

Author: LouisK92

src/methods_cell_type_annotation/moscot/config.vsh.yaml

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

src/methods_transcript_assignment/baysor/script.py

@@ -114,9 +114,12 @@
 
 # Make transcript patches
 sopa.make_transcript_patches(sdata_sopa, patch_width=2000, patch_overlap=50, prior_shapes_key="cell_id")
-sopa.settings.parallelization_backend = "dask"
 
 # Run baysor
+# sopa.settings.parallelization_backend = "dask" #NOTE: didn't lead to high speed, also I think workers kept dying, instead went with JULIA_NUM_THREADS
+n_threads = meta['cpus'] or os.cpu_count()
+n_threads = max(n_threads-2, 1)
+os.environ['JULIA_NUM_THREADS'] = str(n_threads)
 sopa.segmentation.baysor(sdata_sopa, config=str(CONFIG_TOML))
 
 # Assign transcripts to cell ids