diff --git a/params/subsample_200_ridge.yaml b/params/subsample_200_ridge.yaml
index da36ee140..ddb96e055 100644
--- a/params/subsample_200_ridge.yaml
+++ b/params/subsample_200_ridge.yaml
@@ -1,22 +1,321 @@
 param_list:
   - id: pearson_celloracle
-    perturbation_data: resources/grn-benchmark/perturbation_data.h5ad
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
     layer: pearson
-    prediction: resources/grn_models/celloracle.csv 
+    prediction: s3://openproblems-data/resources/grn/grn_models/celloracle.csv 
     reg_type: ridge
     method_id: celloracle
     subsample: 200
     max_workers: 20
 
-  - id: lognorm_positive_control
-    perturbation_data: resources/grn-benchmark/perturbation_data.h5ad
+  - id: lognorm_celloracle
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: lognorm
+    prediction: s3://openproblems-data/resources/grn/grn_models/celloracle.csv 
+    reg_type: ridge
+    method_id: celloracle
+    subsample: 200
+    max_workers: 20
+
+  - id: scgen_pearson_celloracle
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: scgen_pearson
+    prediction: s3://openproblems-data/resources/grn/grn_models/celloracle.csv 
+    reg_type: ridge
+    method_id: celloracle
+    subsample: 200
+    max_workers: 20
+
+  - id: scgen_lognorm_celloracle
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: scgen_lognorm
+    prediction: s3://openproblems-data/resources/grn/grn_models/celloracle.csv 
+    reg_type: ridge
+    method_id: celloracle
+    subsample: 200
+    max_workers: 20
+
+  - id: seurat_pearson_celloracle
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: seurat_pearson
+    prediction: s3://openproblems-data/resources/grn/grn_models/celloracle.csv 
+    reg_type: ridge
+    method_id: celloracle
+    subsample: 200
+    max_workers: 20
+
+  - id: seurat_lognorm_celloracle
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: seurat_lognorm
+    prediction: s3://openproblems-data/resources/grn/grn_models/celloracle.csv 
+    reg_type: ridge
+    method_id: celloracle
+    subsample: 200
+    max_workers: 20
+
+  - id: pearson_scenicplus
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: pearson
+    prediction: s3://openproblems-data/resources/grn/grn_models/scenicplus.csv 
+    reg_type: ridge
+    method_id: scenicplus
+    subsample: 200
+    max_workers: 20
+
+  - id: lognorm_scenicplus
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: lognorm
+    prediction: s3://openproblems-data/resources/grn/grn_models/scenicplus.csv 
+    reg_type: ridge
+    method_id: scenicplus
+    subsample: 200
+    max_workers: 20
+
+  - id: scgen_pearson_scenicplus
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: scgen_pearson
+    prediction: s3://openproblems-data/resources/grn/grn_models/scenicplus.csv 
+    reg_type: ridge
+    method_id: scenicplus
+    subsample: 200
+    max_workers: 20
+
+  - id: scgen_lognorm_scenicplus
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: scgen_lognorm
+    prediction: s3://openproblems-data/resources/grn/grn_models/scenicplus.csv 
+    reg_type: ridge
+    method_id: scenicplus
+    subsample: 200
+    max_workers: 20
+
+  - id: seurat_pearson_scenicplus
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: seurat_pearson
+    prediction: s3://openproblems-data/resources/grn/grn_models/scenicplus.csv 
+    reg_type: ridge
+    method_id: scenicplus
+    subsample: 200
+    max_workers: 20
+
+  - id: seurat_lognorm_scenicplus
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: seurat_lognorm
+    prediction: s3://openproblems-data/resources/grn/grn_models/scenicplus.csv 
+    reg_type: ridge
+    method_id: scenicplus
+    subsample: 200
+    max_workers: 20
+
+  - id: pearson_figr
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: pearson
+    prediction: s3://openproblems-data/resources/grn/grn_models/figr.csv 
+    reg_type: ridge
+    method_id: figr
+    subsample: 200
+    max_workers: 20
+
+  - id: lognorm_figr
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: lognorm
+    prediction: s3://openproblems-data/resources/grn/grn_models/figr.csv 
+    reg_type: ridge
+    method_id: figr
+    subsample: 200
+    max_workers: 20
+
+  - id: scgen_pearson_figr
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: scgen_pearson
+    prediction: s3://openproblems-data/resources/grn/grn_models/figr.csv 
+    reg_type: ridge
+    method_id: figr
+    subsample: 200
+    max_workers: 20
+
+  - id: scgen_lognorm_figr
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: scgen_lognorm
+    prediction: s3://openproblems-data/resources/grn/grn_models/figr.csv 
+    reg_type: ridge
+    method_id: figr
+    subsample: 200
+    max_workers: 20
+
+  - id: seurat_pearson_figr
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: seurat_pearson
+    prediction: s3://openproblems-data/resources/grn/grn_models/figr.csv 
+    reg_type: ridge
+    method_id: figr
+    subsample: 200
+    max_workers: 20
+
+  - id: seurat_lognorm_figr
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: seurat_lognorm
+    prediction: s3://openproblems-data/resources/grn/grn_models/figr.csv 
+    reg_type: ridge
+    method_id: figr
+    subsample: 200
+    max_workers: 20
+
+  - id: pearson_granie
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: pearson
+    prediction: s3://openproblems-data/resources/grn/grn_models/granie.csv 
+    reg_type: ridge
+    method_id: granie
+    subsample: 200
+    max_workers: 20
+
+  - id: lognorm_granie
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: lognorm
+    prediction: s3://openproblems-data/resources/grn/grn_models/granie.csv 
+    reg_type: ridge
+    method_id: granie
+    subsample: 200
+    max_workers: 20
+
+  - id: scgen_pearson_granie
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: scgen_pearson
+    prediction: s3://openproblems-data/resources/grn/grn_models/granie.csv 
+    reg_type: ridge
+    method_id: granie
+    subsample: 200
+    max_workers: 20
+
+  - id: scgen_lognorm_granie
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: scgen_lognorm
+    prediction: s3://openproblems-data/resources/grn/grn_models/granie.csv 
+    reg_type: ridge
+    method_id: granie
+    subsample: 200
+    max_workers: 20
+
+  - id: seurat_pearson_granie
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: seurat_pearson
+    prediction: s3://openproblems-data/resources/grn/grn_models/granie.csv 
+    reg_type: ridge
+    method_id: granie
+    subsample: 200
+    max_workers: 20
+
+  - id: seurat_lognorm_granie
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: seurat_lognorm
+    prediction: s3://openproblems-data/resources/grn/grn_models/granie.csv 
+    reg_type: ridge
+    method_id: granie
+    subsample: 200
+    max_workers: 20
+
+  - id: pearson_scglue
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: pearson
+    prediction: s3://openproblems-data/resources/grn/grn_models/scglue.csv 
+    reg_type: ridge
+    method_id: scglue
+    subsample: 200
+    max_workers: 20
+
+  - id: lognorm_scglue
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: lognorm
+    prediction: s3://openproblems-data/resources/grn/grn_models/scglue.csv 
+    reg_type: ridge
+    method_id: scglue
+    subsample: 200
+    max_workers: 20
+
+  - id: scgen_pearson_scglue
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: scgen_pearson
+    prediction: s3://openproblems-data/resources/grn/grn_models/scglue.csv 
+    reg_type: ridge
+    method_id: scglue
+    subsample: 200
+    max_workers: 20
+
+  - id: scgen_lognorm_scglue
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: scgen_lognorm
+    prediction: s3://openproblems-data/resources/grn/grn_models/scglue.csv 
+    reg_type: ridge
+    method_id: scglue
+    subsample: 200
+    max_workers: 20
+
+  - id: seurat_pearson_scglue
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: seurat_pearson
+    prediction: s3://openproblems-data/resources/grn/grn_models/scglue.csv 
+    reg_type: ridge
+    method_id: scglue
+    subsample: 200
+    max_workers: 20
+
+  - id: seurat_lognorm_scglue
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: seurat_lognorm
+    prediction: s3://openproblems-data/resources/grn/grn_models/scglue.csv 
+    reg_type: ridge
+    method_id: scglue
+    subsample: 200
+    max_workers: 20
+
+  - id: pearson_positive_control
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
     layer: pearson
     reg_type: ridge
     method_id: positive_control
-    tf_all: resources/prior/tf_all.csv
     subsample: 200
     max_workers: 20
 
+  - id: lognorm_positive_control
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: lognorm
+    reg_type: ridge
+    method_id: positive_control
+    subsample: 200
+    max_workers: 20
+
+  - id: scgen_pearson_positive_control
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: scgen_pearson
+    reg_type: ridge
+    method_id: positive_control
+    subsample: 200
+    max_workers: 20
+
+  - id: scgen_lognorm_positive_control
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: scgen_lognorm
+    reg_type: ridge
+    method_id: positive_control
+    subsample: 200
+    max_workers: 20
+
+  - id: seurat_pearson_positive_control
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: seurat_pearson
+    reg_type: ridge
+    method_id: positive_control
+    subsample: 200
+    max_workers: 20
+
+  - id: seurat_lognorm_positive_control
+    perturbation_data: s3://openproblems-data/resources/grn/grn-benchmark/perturbation_data.h5ad
+    layer: seurat_lognorm
+    reg_type: ridge
+    method_id: positive_control
+    subsample: 200
+    max_workers: 20
 
 output_state: "state.yaml"
 publish_dir: "s3://openproblems-data/resources/grn/results/subsample_200_ridge"
diff --git a/scripts/run_grn_evaluation_tw.sh b/scripts/run_grn_evaluation_tw.sh
index 6defe7352..13d78ce2b 100644
--- a/scripts/run_grn_evaluation_tw.sh
+++ b/scripts/run_grn_evaluation_tw.sh
@@ -66,7 +66,8 @@ grn_name="positive_control"
 for layer in "${layers[@]}"; do
   cat >> $param_file << HERE
   - id: ${layer}_${grn_name}
-    perturbation_data: ${perturbation_data}
+    perturbation_data: ${resources_dir}/grn-benchmark/perturbation_data.h5ad
+    tf_all: ${resources_dir}/prior/tf_all.csv
     layer: ${layer}
     reg_type: $reg_type
     method_id: $grn_name
diff --git a/scripts/run_grn_inference.sh b/scripts/run_grn_inference.sh
index cd548d393..7d04c88ab 100644
--- a/scripts/run_grn_inference.sh
+++ b/scripts/run_grn_inference.sh
@@ -28,7 +28,7 @@ HERE
 
 if [ "$submit" = true ]; then
   nextflow run . \
-    -main-script  target/nextflow/workflows/run_grn_inference/main.nf \
+    -main-script  target/nextflow/workflows/grn_inference_celloracle/main.nf \
     -profile docker \
     -with-trace \
     -c src/common/nextflow_helpers/labels_ci.config \
diff --git a/src/methods/multi_omics/celloracle/config.vsh.yaml b/src/methods/multi_omics/celloracle/config.vsh.yaml
index 92219e2a8..21197f9dd 100644
--- a/src/methods/multi_omics/celloracle/config.vsh.yaml
+++ b/src/methods/multi_omics/celloracle/config.vsh.yaml
@@ -8,14 +8,20 @@ functionality:
     summary: "GRN inference using celloracle"
     description: |
       GRN inference using celloracle. 
-    documentation_url: https://morris-lab.github.io/CellOracle.documentation/    
-      
+    documentation_url: https://morris-lab.github.io/CellOracle.documentation/   
+  arguments:
+    - name: --base_grn
+      type: file
+      direction: output
+      default: output/celloracle/base_grn.csv
+    - name: --links
+      type: file
+      direction: output
+      default: output/celloracle/links.celloracle.links
   resources:
     - type: python_script
       path: script.py
     - path: main.py
-
-
 platforms:
   - type: docker
     image: kenjikamimoto126/celloracle_ubuntu:0.18.0
diff --git a/src/methods/multi_omics/celloracle/main.py b/src/methods/multi_omics/celloracle/main.py
index 6184486cb..c27be06b1 100644
--- a/src/methods/multi_omics/celloracle/main.py
+++ b/src/methods/multi_omics/celloracle/main.py
@@ -50,7 +50,7 @@ def base_grn(par) -> None:
 
     df = tfi.to_dataframe()
     print("Base GRN is built")
-    df.to_csv(f"{par['temp_dir']}/grn_celloracle_base.csv")
+    df.to_csv(par['base_grn'])
 
 def preprocess_rna(par) -> None:
     print("Processing rna data")
@@ -102,7 +102,7 @@ def preprocess_rna(par) -> None:
 def infer_grn(par):
     print("Inferring GRN using base GRN and rna expression")
     adata = ad.read_h5ad(f"{par['temp_dir']}/adata.h5ad")
-    base_GRN = pd.read_csv(f"{par['temp_dir']}/grn_celloracle_base.csv")
+    base_GRN = pd.read_csv(par['base_grn'])
     # Instantiate Oracle object
     oracle = co.Oracle()
     # Instantiate Oracle object.
@@ -125,14 +125,15 @@ def infer_grn(par):
                         b_maxl=k*4, n_jobs=par["num_workers"])
     links = oracle.get_links(cluster_name_for_GRN_unit="cell_type", alpha=10,
                         verbose_level=10, n_jobs=par["num_workers"])
-    links.to_hdf5(file_path=f"{par['temp_dir']}/links.celloracle.links")
+    links.to_hdf5(file_path=par['links'])
 def refine_grns(par):
     print("Refining GRNs")
-    links_o = co.load_hdf5(f"{par['temp_dir']}/links.celloracle.links")
+    links_o = co.load_hdf5(par['links'])
     links_dict =  links_o.links_dict.copy()
     grn_stack = []
     tt = 0.05
     for cell_type, grn in links_dict.items():
+        print(f"{cell_type}, GRN before filter: {grn.shape}")
         mask = grn.p<tt # remove insig links
         grn = grn[mask]
         grn = grn[~(grn.coef_abs==0)] # remove those with 0 coeff
diff --git a/src/methods/multi_omics/celloracle/run.sh b/src/methods/multi_omics/celloracle/run.sh
index c4b792e9d..c22db70f7 100644
--- a/src/methods/multi_omics/celloracle/run.sh
+++ b/src/methods/multi_omics/celloracle/run.sh
@@ -1,5 +1,7 @@
-viash run src/methods/celloracle/config.vsh.yaml -- --multiomics_rna resources_test/grn-benchmark/multiomics_rna.h5ad \
+viash run src/methods/multi_omics/celloracle/config.vsh.yaml -- --multiomics_rna resources_test/grn-benchmark/multiomics_rna.h5ad \
     --multiomics_atac resources_test/grn-benchmark/multiomics_atac.h5ad \
     --prediction output/prediction.csv \
+    --links output/celloracle/links.celloracle.links \
+    --base_grn output/celloracle/base_grn.csv \
     --temp_dir output/celloracle/ \
     --num_workers 2
diff --git a/src/methods/multi_omics/celloracle_ns/config.vsh.yaml b/src/methods/multi_omics/celloracle_ns/config.vsh.yaml
new file mode 100644
index 000000000..d38d395e3
--- /dev/null
+++ b/src/methods/multi_omics/celloracle_ns/config.vsh.yaml
@@ -0,0 +1,29 @@
+
+__merge__: ../../../api/comp_method.yaml
+
+functionality:
+  name: grn_inference_celloracle
+  namespace: "workflows"
+  info:
+    label: grn_inference_celloracle
+    summary: "Infers GRNs from multiomics data using celloracle."
+  arguments:
+    - name: --base_grn
+      type: file
+      direction: output
+      default: output/celloracle/base_grn.csv
+    - name: --links
+      type: file
+      direction: output
+      default: output/celloracle/links.celloracle.links
+  resources:
+    - type: nextflow_script
+      path: main.nf
+      entrypoint: run_wf
+  dependencies:
+    - name: grn_methods/celloracle 
+
+platforms:
+  - type: nextflow
+    directives:
+      label: [ midtime, midmem, lowcpu ]
diff --git a/src/methods/multi_omics/celloracle_ns/main.nf b/src/methods/multi_omics/celloracle_ns/main.nf
new file mode 100644
index 000000000..572104cd5
--- /dev/null
+++ b/src/methods/multi_omics/celloracle_ns/main.nf
@@ -0,0 +1,19 @@
+workflow run_wf {
+  take:
+  input_ch
+
+  main:
+  output_ch = input_ch
+
+    | celloracle.run(
+      fromState: [multiomics_rna: "multiomics_rna",
+              multiomics_atac: "multiomics_atac",
+              temp_dir: "temp_dir",
+              num_workers: "num_workers"
+              ],
+      toState: [prediction:"prediction", base_grn: "base_grn", links: "links"]
+    )
+
+  emit:
+  output_ch
+}