update workflows

openproblems-bio · Oct 25, 2024 · bd6507d · bd6507d
1 parent a6f8216
commit bd6507d
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Showing 6 changed files with 7 additions and 48 deletions.
diff --git a/src/workflows/process_datasets/config.vsh.yaml b/src/workflows/process_datasets/config.vsh.yaml
@@ -35,14 +35,9 @@ resources:
     entrypoint: run_wf
   - path: /common/nextflow_helpers/helper.nf
 dependencies:
-  - name: common/check_dataset_schema
-    repository: openproblems_v2
+  - name: schema/verify_data_structure
+    repository: core
   - name: process_dataset/dataset_simulator
   - name: process_dataset/split_dataset
-repositories:
-  - name: openproblems_v2
-    type: github
-    repo: openproblems-bio/openproblems-v2
-    tag: main_build
 runners:
   - type: nextflow
diff --git a/src/workflows/process_datasets/main.nf b/src/workflows/process_datasets/main.nf
@@ -14,7 +14,7 @@ workflow run_wf {
   main:
   output_ch = input_ch
 
-    | check_dataset_schema.run(
+    | verify_data_structure.run(
       fromState: { id, state ->
         def schema = findArgumentSchema(meta.config, "input")
         def schemaYaml = tempFile("schema.yaml")

diff --git a/src/workflows/process_datasets/run_test.sh b/src/workflows/process_datasets/run_test.sh
diff --git a/src/workflows/run_benchmark/config.vsh.yaml b/src/workflows/run_benchmark/config.vsh.yaml
@@ -48,10 +48,8 @@ resources:
     path: main.nf
     entrypoint: run_wf
 dependencies:
-  - name: common/check_dataset_schema
-    repository: openproblems_v2
-  - name: common/extract_metadata
-    repository: openproblems_v2
+  - name: h5ad/extract_uns_metadata
+    repository: core
   - name: control_methods/random_proportions
   - name: control_methods/true_proportions
   - name: methods/cell2location

diff --git a/src/workflows/run_benchmark/main.nf b/src/workflows/run_benchmark/main.nf
@@ -42,7 +42,7 @@ workflow run_wf {
     }
 
     // extract the dataset metadata
-    | extract_metadata.run(
+    | extract_uns_metadata.run(
       fromState: [input: "input_solution"],
       toState: { id, output, state ->
         state + [
@@ -150,7 +150,7 @@ workflow run_wf {
   output_ch = score_ch
 
     // extract the scores
-    | extract_metadata.run(
+    | extract_uns_metadata.run(
       key: "extract_scores",
       fromState: [input: "metric_output"],
       toState: { id, output, state ->

diff --git a/src/workflows/run_benchmark/run_test.sh b/src/workflows/run_benchmark/run_test.sh