Fix/migrate zarr v2 to v3

src/datasets/loaders/bruker_cosmx/config.vsh.yaml

@@ -76,4 +76,4 @@ runners:
   - type: executable
   - type: nextflow
     directives:
-      label: [veryhighmem, midcpu, hightime]
+      label: [midmem, midcpu, hightime]

src/methods_expression_correction/split/config.vsh.yaml

@@ -28,21 +28,22 @@ engines:
     setup:
       - type: docker
         run: |
-          apt-get update
+          apt-get update && apt-get install -y libcurl4-openssl-dev libssl-dev libgit2-dev libxml2-dev
       # - type: r
       #   packages: [fs, rlang, lifecycle]
       - type: r
-        bioc: [SingleCellExperiment, anndataR, rhdf5, devtools, scater]
-        # bioc: [SpatialExperiment, anndataR, rhdf5, devtools, scater]
+        bioc: [SingleCellExperiment, anndataR, rhdf5, scater]
+        # bioc: [SpatialExperiment, anndataR, rhdf5, scater]
 
         # SingleCellExperiment part can probably be left out again in the future. It currently fixes a bug described in these issues:
         # https://github.com/drighelli/SpatialExperiment/issues/171
         # https://github.com/satijalab/seurat/issues/9889
         # The reinstall of SingleCellExperiment triggers the correct re-install of SpatialExperiment.
       - type: r
         github: dmcable/spacexr
-      - type: r
-        github: bdsc-tds/SPLIT
+      - type: docker
+        run: |
+          Rscript -e 'remotes::install_github("bdsc-tds/SPLIT")'
 
   - type: native