Remove table creation in custom segmentation and adjust memory of various methods (#102)

Author: LouisK92

src/control_methods/identity/config.vsh.yaml

@@ -16,4 +16,4 @@ runners:
   - type: executable
   - type: nextflow
     directives:
-      label: [midtime, midmem, lowcpu]
+      label: [midtime, highmem, lowcpu]

src/control_methods/permute_celltype_annotations/config.vsh.yaml

@@ -20,4 +20,4 @@ runners:
   - type: executable
   - type: nextflow
     directives:
-      label: [midtime, midmem, lowcpu]
+      label: [midtime, highmem, lowcpu]

src/methods_segmentation/custom_segmentation/script.py

@@ -23,13 +23,13 @@
 sdata_segmentation_only = sd.SpatialData(
   labels={
     "segmentation": sdata[par["labels_key"]]
-  },
-  tables={
-    "table": ad.AnnData(
-      obs=sdata.tables["table"].obs[["cell_id", "region"]],
-      var=sdata.tables["table"].var[[]]
-    )
-  }
+  }#,
+  #tables={
+  #  "table": ad.AnnData(
+  #    obs=sdata.tables["table"].obs[["cell_id", "region"]],
+  #    var=sdata.tables["table"].var[[]]
+  #  )
+  #}
 )
 
 print("Writing output", flush=True)

src/methods_segmentation/watershed/config.vsh.yaml

@@ -173,5 +173,5 @@ runners:
   - type: executable
   - type: nextflow
     directives:
-      label: [ midtime, midcpu, highmem ]
+      label: [ hightime, midcpu, veryhighmem ]
 

src/metrics/quality/config.vsh.yaml

@@ -42,4 +42,4 @@ runners:
   - type: executable
   - type: nextflow
     directives:
-      label: [midtime, midmem, midcpu]
+      label: [midtime, highmem, midcpu]

src/metrics/similarity/config.vsh.yaml

@@ -101,4 +101,4 @@ runners:
   # Allows turning the component into a Nextflow module / pipeline.
   - type: nextflow
     directives:
-      label: [midtime, midmem, midcpu]
+      label: [midtime, highmem, midcpu]