bump viash version

_viash.yaml

@@ -1,4 +1,4 @@
-viash_version: 0.9.0
+viash_version: 0.9.4
 
 # Step 1: Change the name of the task.
 name: task_cyto_batch_integration
@@ -73,8 +73,7 @@ config_mods: |
   .runners[.type == "nextflow"].config.labels := { lowmem : "memory = 20.Gb", midmem : "memory = 50.Gb", highmem : "memory = 100.Gb", lowcpu : "cpus = 5", midcpu : "cpus = 15", highcpu : "cpus = 30", lowtime : "time = 1.h", midtime : "time = 4.h", hightime : "time = 8.h", veryhightime : "time = 24.h" }
 
 repositories:
-  - name: core
+  - name: op
     type: github
-    repo: openproblems-bio/core
+    repo: openproblems-bio/openproblems
     tag: build/main
-    path: viash/core

src/workflows/process_datasets/config.vsh.yaml

@@ -30,8 +30,8 @@ resources:
   - path: /common/nextflow_helpers/helper.nf
 
 dependencies:
-  - name: schema/verify_data_structure
-    repository: core
+  - name: validation/check_dataset_with_schema
+    repository: openproblems
   - name: data_processors/process_dataset
 
 runners:

src/workflows/process_datasets/main.nf

@@ -14,7 +14,7 @@ workflow run_wf {
   main:
   output_ch = input_ch
 
-    | verify_data_structure.run(
+    | check_dataset_with_schema.run(
       fromState: { id, state ->
         def schema = findArgumentSchema(meta.config, "input")
         def schemaYaml = tempFile("schema.yaml")

src/workflows/run_benchmark/config.vsh.yaml

@@ -61,8 +61,8 @@ resources:
     path: /_viash.yaml
 
 dependencies:
-  - name: h5ad/extract_uns_metadata
-    repository: core
+  - name: utils/extract_uns_metadata
+    repository: op
   - name: control_methods/shuffle_integration
   - name: control_methods/shuffle_integration_by_batch
   - name: control_methods/shuffle_integration_by_cell_type