From cb2d71bc2d3e564a47639843854455ae6e450237 Mon Sep 17 00:00:00 2001
From: Kai Waldrant <kai@data-intuitive.com>
Date: Thu, 19 Sep 2024 11:54:33 +0200
Subject: [PATCH 1/4] fix dependencis process datasets wf

---
 src/workflows/process_datasets/config.vsh.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/workflows/process_datasets/config.vsh.yaml b/src/workflows/process_datasets/config.vsh.yaml
index 6041a5c..0e4004d 100644
--- a/src/workflows/process_datasets/config.vsh.yaml
+++ b/src/workflows/process_datasets/config.vsh.yaml
@@ -26,8 +26,8 @@ dependencies:
   - name: common/check_dataset_schema
     repository:
       type: github
-      repo: openproblems-bio/openproblems-v2
-      tag: main_build
-  - name: process_dataset/process_dataset
+      repo: openproblems-bio/openproblems
+      tag: build/main
+  - name: data_processors/process_dataset
 runners:
   - type: nextflow

From a89ccb15ef84f118655eff890a7e8d63f339f115 Mon Sep 17 00:00:00 2001
From: Kai Waldrant <kai@data-intuitive.com>
Date: Thu, 19 Sep 2024 11:55:51 +0200
Subject: [PATCH 2/4] fix dependencies benchmark wf

---
 src/workflows/run_benchmark/config.vsh.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/workflows/run_benchmark/config.vsh.yaml b/src/workflows/run_benchmark/config.vsh.yaml
index da35f2b..234bbe8 100644
--- a/src/workflows/run_benchmark/config.vsh.yaml
+++ b/src/workflows/run_benchmark/config.vsh.yaml
@@ -53,9 +53,9 @@ resources:
     path: /_viash.yaml
 dependencies:
   - name: common/check_dataset_schema
-    repository: openproblems-v2
+    repository: openproblems
   - name: common/extract_metadata
-    repository: openproblems-v2
+    repository: openproblems
   - name: control_methods/no_denoising
   - name: control_methods/perfect_denoising
   - name: methods/alra
@@ -65,9 +65,9 @@ dependencies:
   - name: metrics/mse
   - name: metrics/poisson
 repositories:
-  - name: openproblems-v2
+  - name: openproblems
     type: github
-    repo: openproblems-bio/openproblems-v2
-    tag: main_build
+    repo: openproblems-bio/openproblems
+    tag: build/main
 runners:
   - type: nextflow

From ecca414b36145a6dc6dfe7ea8b60524b9eee4e1b Mon Sep 17 00:00:00 2001
From: Kai Waldrant <kai@data-intuitive.com>
Date: Thu, 19 Sep 2024 11:58:26 +0200
Subject: [PATCH 3/4] update changelog

---
 CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6c817fb..b220bab 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -32,6 +32,10 @@
 
 * Small changes to api file names (PR #13).
 
+## BUG FIXES
+
+* Update the nextflow workflow dependencies (PR #17).
+
 
 ## transfer from openproblems-v2 repository
 

From eef6d6d17f9b6f5978ffdf5130fc6e04d7c3cff4 Mon Sep 17 00:00:00 2001
From: Kai Waldrant <kai@data-intuitive.com>
Date: Thu, 19 Sep 2024 14:17:44 +0200
Subject: [PATCH 4/4] Move dependency reposotry to viash config

---
 _viash.yaml                                    | 6 ++++++
 src/workflows/process_datasets/config.vsh.yaml | 5 +----
 src/workflows/run_benchmark/config.vsh.yaml    | 5 -----
 3 files changed, 7 insertions(+), 9 deletions(-)

diff --git a/_viash.yaml b/_viash.yaml
index 218e5a1..3a3b5ff 100644
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -71,6 +71,12 @@ authors:
       github: KaiWaldrant
       orcid: "0009-0003-8555-1361"
 
+repositories:
+  - name: openproblems
+    type: github
+    repo: openproblems-bio/openproblems
+    tag: build/main
+
 viash_version: 0.9.0
 
 config_mods: |
diff --git a/src/workflows/process_datasets/config.vsh.yaml b/src/workflows/process_datasets/config.vsh.yaml
index 0e4004d..3d283dd 100644
--- a/src/workflows/process_datasets/config.vsh.yaml
+++ b/src/workflows/process_datasets/config.vsh.yaml
@@ -24,10 +24,7 @@ resources:
   - path: /common/nextflow_helpers/helper.nf
 dependencies:
   - name: common/check_dataset_schema
-    repository:
-      type: github
-      repo: openproblems-bio/openproblems
-      tag: build/main
+    repository: openproblems
   - name: data_processors/process_dataset
 runners:
   - type: nextflow
diff --git a/src/workflows/run_benchmark/config.vsh.yaml b/src/workflows/run_benchmark/config.vsh.yaml
index 234bbe8..1d408ee 100644
--- a/src/workflows/run_benchmark/config.vsh.yaml
+++ b/src/workflows/run_benchmark/config.vsh.yaml
@@ -64,10 +64,5 @@ dependencies:
   - name: methods/magic
   - name: metrics/mse
   - name: metrics/poisson
-repositories:
-  - name: openproblems
-    type: github
-    repo: openproblems-bio/openproblems
-    tag: build/main
 runners:
   - type: nextflow