Migrate from core to openproblems (#11)

* switch from core to openproblems

* fix script

_viash.yaml

@@ -88,6 +88,5 @@ config_mods: |
 repositories:
   - name: core
     type: github
-    repo: openproblems-bio/core
+    repo: openproblems-bio/openproblems
     tag: build/main
-    path: viash/core

scripts/run_benchmark/run_test_seqeracloud.sh

@@ -13,7 +13,7 @@ cat > /tmp/params.yaml << 'HERE'
 input_states: s3://openproblems-data/resources_test/task_batch_integration/**/state.yaml
 rename_keys: 'input_dataset:output_dataset;input_solution:output_solution'
 output_state: "state.yaml"
-publish_dir: s3://openproblems-nextflow/temp/task_batch_integration/
+publish_dir: s3://openproblems-work/temp/task_batch_integration/
 HERE
 
 tw launch https://github.com/openproblems-bio/task_batch_integration.git \

src/workflows/process_datasets/config.vsh.yaml

@@ -26,8 +26,8 @@ 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

@@ -70,8 +70,8 @@ resources:
   - path: /common/nextflow_helpers/helper.nf
 
 dependencies:
-  - name: h5ad/extract_uns_metadata
-    repository: core
+  - name: utils/extract_uns_metadata
+    repository: openproblems
   # control methods
   - name: control_methods/embed_cell_types
   - name: control_methods/embed_cell_types_jittered