diff --git a/params/celloracle_test.yaml b/params/celloracle_test.yaml
deleted file mode 100644
index f59ebd3bc..000000000
--- a/params/celloracle_test.yaml
+++ /dev/null
@@ -1,8 +0,0 @@
-param_list:
-  - id: celloracle_test
-    multiomics_rna: s3://openproblems-data/resources_test/grn//grn-benchmark/multiomics_rna.h5ad
-    multiomics_atac: s3://openproblems-data/resources_test/grn//grn-benchmark/multiomics_atac.h5ad
-    num_workers: 20
-    temp_dir: ./tmp/grn
-output_state: "state.yaml"
-publish_dir: "s3://openproblems-data/resources/grn/results/celloracle_test"
diff --git a/params/subsample_200_ridge.yaml b/params/subsample_200_ridge.yaml
index b0503302d..7d6ddfafb 100644
--- a/params/subsample_200_ridge.yaml
+++ b/params/subsample_200_ridge.yaml
@@ -6,7 +6,7 @@ param_list:
     method_id: celloracle
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/celloracle.csv
   - id: lognorm_celloracle
@@ -16,7 +16,7 @@ param_list:
     method_id: celloracle
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/celloracle.csv
   - id: scgen_pearson_celloracle
@@ -26,7 +26,7 @@ param_list:
     method_id: celloracle
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/celloracle.csv
   - id: scgen_lognorm_celloracle
@@ -36,7 +36,7 @@ param_list:
     method_id: celloracle
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/celloracle.csv
   - id: seurat_pearson_celloracle
@@ -46,7 +46,7 @@ param_list:
     method_id: celloracle
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/celloracle.csv
   - id: seurat_lognorm_celloracle
@@ -56,7 +56,7 @@ param_list:
     method_id: celloracle
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/celloracle.csv
   - id: pearson_scenicplus
@@ -66,7 +66,7 @@ param_list:
     method_id: scenicplus
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/scenicplus.csv
   - id: lognorm_scenicplus
@@ -76,7 +76,7 @@ param_list:
     method_id: scenicplus
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/scenicplus.csv
   - id: scgen_pearson_scenicplus
@@ -86,7 +86,7 @@ param_list:
     method_id: scenicplus
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/scenicplus.csv
   - id: scgen_lognorm_scenicplus
@@ -96,7 +96,7 @@ param_list:
     method_id: scenicplus
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/scenicplus.csv
   - id: seurat_pearson_scenicplus
@@ -106,7 +106,7 @@ param_list:
     method_id: scenicplus
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/scenicplus.csv
   - id: seurat_lognorm_scenicplus
@@ -116,7 +116,7 @@ param_list:
     method_id: scenicplus
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/scenicplus.csv
   - id: pearson_figr
@@ -126,7 +126,7 @@ param_list:
     method_id: figr
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/figr.csv
   - id: lognorm_figr
@@ -136,7 +136,7 @@ param_list:
     method_id: figr
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/figr.csv
   - id: scgen_pearson_figr
@@ -146,7 +146,7 @@ param_list:
     method_id: figr
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/figr.csv
   - id: scgen_lognorm_figr
@@ -156,7 +156,7 @@ param_list:
     method_id: figr
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/figr.csv
   - id: seurat_pearson_figr
@@ -166,7 +166,7 @@ param_list:
     method_id: figr
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/figr.csv
   - id: seurat_lognorm_figr
@@ -176,7 +176,7 @@ param_list:
     method_id: figr
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/figr.csv
   - id: pearson_granie
@@ -186,7 +186,7 @@ param_list:
     method_id: granie
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/granie.csv
   - id: lognorm_granie
@@ -196,7 +196,7 @@ param_list:
     method_id: granie
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/granie.csv
   - id: scgen_pearson_granie
@@ -206,7 +206,7 @@ param_list:
     method_id: granie
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/granie.csv
   - id: scgen_lognorm_granie
@@ -216,7 +216,7 @@ param_list:
     method_id: granie
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/granie.csv
   - id: seurat_pearson_granie
@@ -226,7 +226,7 @@ param_list:
     method_id: granie
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/granie.csv
   - id: seurat_lognorm_granie
@@ -236,7 +236,7 @@ param_list:
     method_id: granie
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/granie.csv
   - id: pearson_scglue
@@ -246,7 +246,7 @@ param_list:
     method_id: scglue
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/scglue.csv
   - id: lognorm_scglue
@@ -256,7 +256,7 @@ param_list:
     method_id: scglue
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/scglue.csv
   - id: scgen_pearson_scglue
@@ -266,7 +266,7 @@ param_list:
     method_id: scglue
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/scglue.csv
   - id: scgen_lognorm_scglue
@@ -276,7 +276,7 @@ param_list:
     method_id: scglue
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/scglue.csv
   - id: seurat_pearson_scglue
@@ -286,7 +286,7 @@ param_list:
     method_id: scglue
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/scglue.csv
   - id: seurat_lognorm_scglue
@@ -296,7 +296,7 @@ param_list:
     method_id: scglue
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     prediction: s3://openproblems-data/resources/grn/grn_models/scglue.csv
   - id: seurat_lognorm_negative_control
@@ -306,7 +306,7 @@ param_list:
     method_id: negative_control
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     
     
   - id: pearson_positive_control
@@ -316,7 +316,7 @@ param_list:
     method_id: positive_control
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     tf_all: s3://openproblems-data/resources/grn/prior/tf_all.csv
     
   - id: lognorm_positive_control
@@ -326,7 +326,7 @@ param_list:
     method_id: positive_control
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     tf_all: s3://openproblems-data/resources/grn/prior/tf_all.csv
     
   - id: scgen_pearson_positive_control
@@ -336,7 +336,7 @@ param_list:
     method_id: positive_control
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     tf_all: s3://openproblems-data/resources/grn/prior/tf_all.csv
     
   - id: scgen_lognorm_positive_control
@@ -346,7 +346,7 @@ param_list:
     method_id: positive_control
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     tf_all: s3://openproblems-data/resources/grn/prior/tf_all.csv
     
   - id: seurat_pearson_positive_control
@@ -356,7 +356,7 @@ param_list:
     method_id: positive_control
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     tf_all: s3://openproblems-data/resources/grn/prior/tf_all.csv
     
   - id: seurat_lognorm_positive_control
@@ -366,7 +366,7 @@ param_list:
     method_id: positive_control
     subsample: 200
     max_workers: 20
-    consensus: s3://openproblems-data/resources/grn/prior/consensus.csv
+    consensus: s3://openproblems-data/resources/grn/prior/consensus-num-regulators.json
     tf_all: s3://openproblems-data/resources/grn/prior/tf_all.csv
     
 output_state: "state.yaml"
diff --git a/scripts/run_grn_evaluation_tw.sh b/scripts/run_grn_evaluation_tw.sh
index 030ae0eeb..0f4378452 100644
--- a/scripts/run_grn_evaluation_tw.sh
+++ b/scripts/run_grn_evaluation_tw.sh
@@ -38,7 +38,7 @@ append_entry() {
     method_id: $1
     subsample: $subsample
     max_workers: $max_workers
-    consensus: ${resources_dir}/prior/consensus.json
+    consensus: ${resources_dir}/prior/consensus-num-regulators.json
     ${2:+tf_all: ${resources_dir}/prior/tf_all.csv}
     ${3:+prediction: ${resources_dir}/grn_models/$1.csv}
 HERE
@@ -66,29 +66,21 @@ output_state: "state.yaml"
 publish_dir: "$publish_dir"
 HERE
 
-if [ "$submit" = true ]; then
-  nextflow run . \
-    -main-script  target/nextflow/workflows/run_grn_evaluation/main.nf \
-    -profile docker \
-    -with-trace \
-    -c src/common/nextflow_helpers/labels_ci.config \
-    -params-file ${param_file}
-
-  ./tw-windows-x86_64.exe launch `
-      https://github.com/openproblems-bio/task_grn_benchmark.git `
-      --revision build/main `
-      --pull-latest `
-      --main-script target/nextflow/workflows/run_grn_evaluation/main.nf `
-      --workspace 53907369739130 `
-      --compute-env 6TeIFgV5OY4pJCk8I0bfOh `
-      --params-file ./params/subsample_200_ridge.yaml `
-      --config src/common/nextflow_helpers/labels_tw.config
-
-fi
-
-    
-if [ "$read_results" = true ]; then 
-    aws s3 sync s3://openproblems-data/resources/grn/results/${RUN_ID} ./resources/results/${RUN_ID} 
-fi
+# nextflow run . \
+#   -main-script  target/nextflow/workflows/run_grn_evaluation/main.nf \
+#   -profile docker \
+#   -with-trace \
+#   -c src/common/nextflow_helpers/labels_ci.config \
+#   -params-file ${param_file}
+
+./tw-windows-x86_64.exe launch `
+    https://github.com/openproblems-bio/task_grn_benchmark.git `
+    --revision build/main `
+    --pull-latest `
+    --main-script target/nextflow/workflows/run_grn_evaluation/main.nf `
+    --workspace 53907369739130 `
+    --compute-env 6TeIFgV5OY4pJCk8I0bfOh `
+    --params-file ./params/subsample_200_ridge.yaml `
+    --config src/common/nextflow_helpers/labels_tw.config
 
 
diff --git a/src/methods/multi_omics/celloracle_ns/run.sh b/src/methods/multi_omics/celloracle_ns/run.sh
index 7d04c88ab..96dc51eab 100644
--- a/src/methods/multi_omics/celloracle_ns/run.sh
+++ b/src/methods/multi_omics/celloracle_ns/run.sh
@@ -53,3 +53,12 @@ if [ "$read_results" = true ]; then
 fi
 
 
+# ./tw-windows-x86_64.exe launch `
+#        https://github.com/openproblems-bio/task_grn_benchmark.git `
+#        --revision build/main `
+#        --pull-latest `
+#        --main-script target/nextflow/workflows/grn_inference_celloracle/main.nf `
+#        --workspace 53907369739130 `
+#        --compute-env 6TeIFgV5OY4pJCk8I0bfOh `
+#        --params-file ./params/celloracle.yaml `
+#        --config src/common/nextflow_helpers/labels_tw.config
\ No newline at end of file
diff --git a/src/methods/multi_omics/scglue/main.py b/src/methods/multi_omics/scglue/main.py
index 14e86d053..e2f2ddf42 100644
--- a/src/methods/multi_omics/scglue/main.py
+++ b/src/methods/multi_omics/scglue/main.py
@@ -9,7 +9,7 @@
 import pandas as pd
 import numpy as np
 from ast import literal_eval
-
+import requests
 
 def preprocess(rna, atac, par):
     rna.layers["counts"] = rna.X.copy()
@@ -244,6 +244,23 @@ def cis_inference(par):
     else:
         print("pyscenic ctx failed with return code", result.returncode)
 
+# def download_prior(par):
+#     # get gene annotation
+#     response = requests.get("https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_45/gencode.v45.annotation.gtf.gz")
+#     par['annotation_file'] = f"{par['temp_dir']}/gencode.v45.annotation.gtf.gz"
+#     if response.status_code == 200:
+#         # Write the content to a file
+#         with open(par['annotation_file'], 'wb') as file:
+#             file.write(response.content)
+#         print(f"File downloaded and saved as gencode.v45.annotation.gtf.gz")
+#     else:
+#         print(f"Failed to download the gencode.v45.annotation.gtf.gz. Status code: {response.status_code}")
+
+
+    
+#     annotation_file
+
+
 def main(par):
     os.makedirs(par['temp_dir'], exist_ok=True)
     print('Reading input files', flush=True)
diff --git a/src/methods/multi_omics/scglue_ns/run.sh b/src/methods/multi_omics/scglue_ns/run.sh
index f318d03b3..6d96f4f26 100644
--- a/src/methods/multi_omics/scglue_ns/run.sh
+++ b/src/methods/multi_omics/scglue_ns/run.sh
@@ -1,9 +1,6 @@
 #!/bin/bash
 
 # RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)"
-submit=false
-read_results=true
-
 RUN_ID="scglue"
 resources_dir="s3://openproblems-data/resources/grn/"
 publish_dir="s3://openproblems-data/resources/grn/results/${RUN_ID}"
@@ -17,11 +14,22 @@ param_list:
   - id: ${RUN_ID}
     multiomics_rna: ${resources_dir}/grn-benchmark/multiomics_rna.h5ad
     multiomics_atac: ${resources_dir}/grn-benchmark/multiomics_atac.h5ad
-    annotation_file: ${resources_dir}/supplements/gencode.v45.annotation.gtf.gz
-    motif_file: ${resources_dir}/supplements/JASPAR2022-hg38.bed.gz
+    annotation_file: ${resources_dir}/supplementary/gencode.v45.annotation.gtf.gz
+    motif_file: ${resources_dir}/supplementary/JASPAR2022-hg38.bed.gz
     num_workers: $num_workers
     temp_dir: ./tmp/grn
 output_state: "state.yaml"
 publish_dir: "$publish_dir"
 HERE
 
+
+
+./tw-windows-x86_64.exe launch `
+       https://github.com/openproblems-bio/task_grn_benchmark.git `
+       --revision build/main `
+       --pull-latest `
+       --main-script target/nextflow/workflows/grn_inference_scglue/main.nf `
+       --workspace 53907369739130 `
+       --compute-env 6TeIFgV5OY4pJCk8I0bfOh `
+       --params-file ./params/scglue.yaml `
+       --config src/common/nextflow_helpers/labels_tw.config
\ No newline at end of file
diff --git a/src/metrics/regression_2/config.vsh.yaml b/src/metrics/regression_2/config.vsh.yaml
index 387173d99..51612396c 100644
--- a/src/metrics/regression_2/config.vsh.yaml
+++ b/src/metrics/regression_2/config.vsh.yaml
@@ -21,7 +21,7 @@ platforms:
     image: ghcr.io/openproblems-bio/base_python:1.0.4
     setup:
       - type: python
-        packages: [ lightgbm ]
+        packages: [ lightgbm==4.3.0, numpy==1.26.4 ]
   - type: nextflow
     directives:
       label: [ midtime, highmem, highcpu ]
\ No newline at end of file
diff --git a/src/metrics/regression_2/script.py b/src/metrics/regression_2/script.py
index a51bc059b..ae33a43b1 100644
--- a/src/metrics/regression_2/script.py
+++ b/src/metrics/regression_2/script.py
@@ -28,6 +28,7 @@
 output = main(par)
 
 print('Write output to file', flush=True)
+print(output)
 metric_ids = output.columns.to_numpy()
 metric_values = output.values[0]
 
diff --git a/src/workflows/process_perturbation/config.vsh.yaml b/src/workflows/process_perturbation/config.vsh.yaml
index 6de93351b..d7e52ad42 100644
--- a/src/workflows/process_perturbation/config.vsh.yaml
+++ b/src/workflows/process_perturbation/config.vsh.yaml
@@ -18,7 +18,7 @@ functionality:
 
     - name: --perturbation_data_bc
       __merge__: ../../api/file_perturbation_h5ad.yaml
-      required: true
+      required: false
       direction: output