update viash and repos (#12)

Author: rcannood

CHANGELOG.md

@@ -18,6 +18,10 @@
 
 * Updated configs, components and CI to the latest Viash version (PR #8).
 
+* Updated to Viash 0.9.4 (PR #12).
+
+* Use dependencies in `openproblems-bio/openproblems` (PR #12).
+
 ## MINOR CHANGES
 
 * Updated `README.md` (PR #5).

_viash.yaml

@@ -1,4 +1,4 @@
-viash_version: 0.9.0
+viash_version: 0.9.4
 
 # Step 1: Change the name of the task.
 # example: task_name_of_this_task
@@ -75,14 +75,14 @@ authors:
       linkedin: johndoe
 
 # Step 7: Remove all of the comments of the steps you completed
-# Step 8: High five yourself!
 
 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
-    tag: build/main
-    path: viash/core
+    repo: openproblems-bio/openproblems
+    tag: build/main # Step 8: Set this to the latest release
+
+# Step 9: High five yourself!

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

@@ -62,8 +62,8 @@ resources:
     path: /_viash.yaml
 
 dependencies:
-  - name: h5ad/extract_uns_metadata
-    repository: core
+  - name: utils/extract_uns_metadata
+    repository: op
   - name: control_methods/true_labels
   - name: methods/logistic_regression
   - name: metrics/accuracy