From 405ea6275fc2aabcb068f9f006f548b1c7f5363d Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Sat, 7 Sep 2024 17:52:58 +0200
Subject: [PATCH] update workflows

---
 _viash.yaml                                    | 7 ++++---
 src/workflows/process_datasets/config.vsh.yaml | 6 ++----
 src/workflows/process_datasets/main.nf         | 2 +-
 src/workflows/run_benchmark/config.vsh.yaml    | 6 ++----
 src/workflows/run_benchmark/main.nf            | 2 +-
 5 files changed, 10 insertions(+), 13 deletions(-)

diff --git a/_viash.yaml b/_viash.yaml
index 8674132..fe4c625 100644
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -81,7 +81,8 @@ 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: openproblems-v2
+  - name: core
     type: github
-    repo: openproblems-bio/openproblems-v2
-    tag: main_build
\ No newline at end of file
+    repo: openproblems-bio/core
+    tag: build/main
+    path: viash/core
diff --git a/src/workflows/process_datasets/config.vsh.yaml b/src/workflows/process_datasets/config.vsh.yaml
index 71c1b9b..24d03a7 100644
--- a/src/workflows/process_datasets/config.vsh.yaml
+++ b/src/workflows/process_datasets/config.vsh.yaml
@@ -30,10 +30,8 @@ resources:
   - path: /common/nextflow_helpers/helper.nf
 
 dependencies:
-  - name: common/check_dataset_schema
-    repository: openproblems-v2
-  - name: common/extract_metadata
-    repository: openproblems-v2
+  - name: schema/verify_data_structure
+    repository: core
   - name: data_processors/process_dataset
 
 runners:
diff --git a/src/workflows/process_datasets/main.nf b/src/workflows/process_datasets/main.nf
index eae19f7..8ffa666 100644
--- 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/run_benchmark/config.vsh.yaml b/src/workflows/run_benchmark/config.vsh.yaml
index 12a4602..6b3a3d5 100644
--- a/src/workflows/run_benchmark/config.vsh.yaml
+++ b/src/workflows/run_benchmark/config.vsh.yaml
@@ -62,10 +62,8 @@ resources:
     path: /_viash.yaml
 
 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/true_labels
   - name: methods/logistic_regression
   - name: metrics/accuracy
diff --git a/src/workflows/run_benchmark/main.nf b/src/workflows/run_benchmark/main.nf
index 58183a2..2ea9016 100644
--- a/src/workflows/run_benchmark/main.nf
+++ b/src/workflows/run_benchmark/main.nf
@@ -32,7 +32,7 @@ workflow run_wf {
     }
 
     // extract the dataset metadata
-    | extract_metadata.run(
+    | extract_uns_metadata.run(
       fromState: [input: "input_solution"],
       toState: { id, output, state ->
         state + [