diff --git a/src/methods/multi_omics/celloracle_ns/config.novsh.yaml b/src/methods/multi_omics/celloracle_ns/config.novsh.yaml
new file mode 100644
index 000000000..d38d395e3
--- /dev/null
+++ b/src/methods/multi_omics/celloracle_ns/config.novsh.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..e224f438e
--- /dev/null
+++ b/src/methods/multi_omics/celloracle_ns/main.nf
@@ -0,0 +1,21 @@
+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"]
+    )
+
+    | setState(["prediction", "base_grn", "links"])
+
+  emit:
+  output_ch
+}
diff --git a/src/methods/multi_omics/celloracle_ns/run.sh b/src/methods/multi_omics/celloracle_ns/run.sh
new file mode 100644
index 000000000..bd5b3160a
--- /dev/null
+++ b/src/methods/multi_omics/celloracle_ns/run.sh
@@ -0,0 +1,61 @@
+#!/bin/bash
+
+# RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)"
+RUN_ID="celloracle"
+resources_dir="s3://openproblems-data/resources/grn"
+publish_dir="s3://openproblems-data/resources/grn/results/${RUN_ID}"
+
+# resources_dir="./resources_test"
+# publish_dir="./output/${RUN_ID}"
+
+num_workers=20
+
+param_file="./params/${RUN_ID}.yaml"
+# Start writing to the YAML file
+cat > $param_file << HERE
+param_list:
+  - id: ${RUN_ID}
+    multiomics_rna: ${resources_dir}/grn-benchmark/multiomics_rna.h5ad
+    multiomics_atac: ${resources_dir}/grn-benchmark/multiomics_atac.h5ad
+    num_workers: $num_workers
+    temp_dir: ./tmp/grn
+output_state: "state.yaml"
+publish_dir: "$publish_dir"
+HERE
+
+if [ "$submit" = true ]; then
+  nextflow run . \
+    -main-script  target/nextflow/workflows/grn_inference_celloracle/main.nf \
+    -profile docker \
+    -with-trace \
+    -c src/common/nextflow_helpers/labels_ci.config \
+    -params-file params/${RUN_ID}.yaml
+
+
+  ./tw-windows-x86_64.exe launch `
+        https://github.com/openproblems-bio/task_grn_inference.git `
+        --revision build/main `
+        --pull-latest `
+        --main-script target/nextflow/workflows/run_grn_inference/main.nf `
+        --workspace 53907369739130 `
+        --compute-env 6TeIFgV5OY4pJCk8I0bfOh `
+        --params-file ./params/celloracle_test.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
+
+
+./tw-windows-x86_64.exe launch `
+       https://github.com/openproblems-bio/task_grn_inference.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/granie_ns/config.novsh.yaml b/src/methods/multi_omics/granie_ns/config.novsh.yaml
new file mode 100644
index 000000000..4e005399e
--- /dev/null
+++ b/src/methods/multi_omics/granie_ns/config.novsh.yaml
@@ -0,0 +1,27 @@
+
+__merge__: ../../../api/comp_method_r.yaml
+
+functionality:
+  name: grn_inference_granie
+  namespace: "workflows"
+  info:
+    label: grn_inference_granie
+    summary: "Infers GRNs from multiomics data using granie."
+  arguments:
+    - name: --subset
+      type: boolean
+      required: false
+      default: false
+      direction: input
+
+  resources:
+    - type: nextflow_script
+      path: main.nf
+      entrypoint: run_wf
+  dependencies:
+    - name: grn_methods/granie 
+
+platforms:
+  - type: nextflow
+    directives:
+      label: [ hightime, midmem, highcpu ]
diff --git a/src/methods/multi_omics/granie_ns/main.nf b/src/methods/multi_omics/granie_ns/main.nf
new file mode 100644
index 000000000..9bef84115
--- /dev/null
+++ b/src/methods/multi_omics/granie_ns/main.nf
@@ -0,0 +1,22 @@
+workflow run_wf {
+  take:
+  input_ch
+
+  main:
+  output_ch = input_ch
+
+    | granie.run(
+      fromState: [
+              multiomics_rna_r: "multiomics_rna_r",
+              multiomics_atac_r: "multiomics_atac_r",
+              num_workers: "num_workers",
+              subset: "subset"
+              ],
+      toState: [prediction:"prediction"]
+    )
+
+    | setState(["prediction"])
+
+  emit:
+  output_ch
+}
diff --git a/src/methods/multi_omics/granie_ns/run.sh b/src/methods/multi_omics/granie_ns/run.sh
new file mode 100644
index 000000000..9ee2b676f
--- /dev/null
+++ b/src/methods/multi_omics/granie_ns/run.sh
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+# RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)"
+RUN_ID="scglue"
+resources_dir="s3://openproblems-data/resources/grn"
+publish_dir="s3://openproblems-data/resources/grn/results/${RUN_ID}"
+
+num_workers=20
+
+param_file="./params/${RUN_ID}.yaml"
+
+cat > $param_file << HERE
+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}/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_inference.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/methods/multi_omics/scenicplus_ns/config.novsh.yaml b/src/methods/multi_omics/scenicplus_ns/config.novsh.yaml
new file mode 100644
index 000000000..ac7060938
--- /dev/null
+++ b/src/methods/multi_omics/scenicplus_ns/config.novsh.yaml
@@ -0,0 +1,39 @@
+
+__merge__: ../../../api/comp_method.yaml
+
+functionality:
+  name: grn_inference_scenicplus
+  namespace: "workflows"
+  info:
+    label: grn_inference_scenicplus
+    summary: "Infers GRNs from multiomics data using scenicplus."
+  arguments:
+    - name: --scplus_mdata
+      type: file
+      required: false
+      direction: output
+      description: "Main output object."
+      default: "scplus_mdata.h5mu"
+    - name: --qc
+      type: boolean
+      default: false
+      description: "Whether to perform quality control."
+    - name: --cell_topic
+      type: file 
+      default: output/cell_topic.csv
+      required: false
+      direction: output
+      description: "Cell-topics prob scores"
+
+
+  resources:
+    - type: nextflow_script
+      path: main.nf
+      entrypoint: run_wf
+  dependencies:
+    - name: grn_methods/scenicplus 
+
+platforms:
+  - type: nextflow
+    directives:
+      label: [ midtime, highmem, highcpu ]
diff --git a/src/methods/multi_omics/scenicplus_ns/main.nf b/src/methods/multi_omics/scenicplus_ns/main.nf
new file mode 100644
index 000000000..4a27b82d0
--- /dev/null
+++ b/src/methods/multi_omics/scenicplus_ns/main.nf
@@ -0,0 +1,23 @@
+workflow run_wf {
+  take:
+  input_ch
+
+  main:
+  output_ch = input_ch
+
+    | scenicplus.run(
+      fromState: [
+              multiomics_rna: "multiomics_rna",
+              multiomics_atac: "multiomics_atac",
+              temp_dir: "temp_dir",
+              num_workers: "num_workers"
+              
+              ],
+      toState: [prediction:"prediction", cell_topic:"cell_topic", scplus_mdata:"scplus_mdata"]
+    )
+
+    | setState(["prediction", "cell_topic", "scplus_mdata"])
+
+  emit:
+  output_ch
+}
diff --git a/src/methods/multi_omics/scenicplus_ns/run.sh b/src/methods/multi_omics/scenicplus_ns/run.sh
new file mode 100644
index 000000000..eef0d8c0a
--- /dev/null
+++ b/src/methods/multi_omics/scenicplus_ns/run.sh
@@ -0,0 +1,44 @@
+#!/bin/bash
+
+RUN_ID="scenicplus"
+resources_dir="s3://openproblems-data/resources_test/grn"
+publish_dir="s3://openproblems-data/resources_test/grn/results/${RUN_ID}"
+
+# resources_dir="./resources_test"
+# publish_dir="./output/${RUN_ID}"
+
+num_workers=10
+
+param_file="./params/${RUN_ID}.yaml"
+# Start writing to the YAML file
+cat > $param_file << HERE
+param_list:
+  - id: ${RUN_ID}
+    multiomics_rna: ${resources_dir}/grn-benchmark/multiomics_rna.h5ad
+    multiomics_atac: ${resources_dir}/grn-benchmark/multiomics_atac.h5ad
+    num_workers: $num_workers
+    temp_dir: tmp/grn
+output_state: "state.yaml"
+publish_dir: "$publish_dir"
+HERE
+
+
+nextflow run . \
+  -main-script  target/nextflow/workflows/grn_inference_scenicplus/main.nf \
+  -profile docker \
+  -with-trace \
+  -c src/common/nextflow_helpers/labels_ci.config \
+  -params-file params/${RUN_ID}.yaml
+
+
+# ./tw-windows-x86_64.exe launch `
+#       https://github.com/openproblems-bio/task_grn_inference.git `
+#       --revision build/main `
+#       --pull-latest `
+#       --main-script target/nextflow/workflows/grn_inference_scenicplus/main.nf `
+#       --workspace 53907369739130 `
+#       --compute-env 6TeIFgV5OY4pJCk8I0bfOh `
+#       --params-file ./params/scenicplus.yaml `
+#       --config src/common/nextflow_helpers/labels_tw.config
+
+
diff --git a/src/methods/multi_omics/scglue_ns/config.novsh.yaml b/src/methods/multi_omics/scglue_ns/config.novsh.yaml
new file mode 100644
index 000000000..805bc8b5b
--- /dev/null
+++ b/src/methods/multi_omics/scglue_ns/config.novsh.yaml
@@ -0,0 +1,29 @@
+
+__merge__: ../../../api/comp_method.yaml
+
+functionality:
+  name: grn_inference_scglue
+  namespace: "workflows"
+  info:
+    label: grn_inference_scglue
+    summary: "Infers GRNs from multiomics data using scglue."
+  arguments:
+    - name: --annotation_file
+      type: file
+      required: true
+      direction: input
+    - name: --motif_file
+      type: file
+      required: true
+      direction: input
+  resources:
+    - type: nextflow_script
+      path: main.nf
+      entrypoint: run_wf
+  dependencies:
+    - name: grn_methods/scglue 
+
+platforms:
+  - type: nextflow
+    directives:
+      label: [oneweektime,midmem,highcpu]
diff --git a/src/methods/multi_omics/scglue_ns/main.nf b/src/methods/multi_omics/scglue_ns/main.nf
new file mode 100644
index 000000000..bc58828cd
--- /dev/null
+++ b/src/methods/multi_omics/scglue_ns/main.nf
@@ -0,0 +1,23 @@
+workflow run_wf {
+  take:
+  input_ch
+
+  main:
+  output_ch = input_ch
+
+    | scglue.run(
+      fromState: [multiomics_rna: "multiomics_rna",
+              multiomics_atac: "multiomics_atac",
+              temp_dir: "temp_dir",
+              num_workers: "num_workers",
+              annotation_file: "annotation_file",
+              motif_file: "motif_file"
+              ],
+      toState: [prediction:"prediction"]
+    )
+
+    | setState(["prediction"])
+
+  emit:
+  output_ch
+}
diff --git a/src/methods/multi_omics/scglue_ns/run.sh b/src/methods/multi_omics/scglue_ns/run.sh
new file mode 100644
index 000000000..6677eb0d3
--- /dev/null
+++ b/src/methods/multi_omics/scglue_ns/run.sh
@@ -0,0 +1,34 @@
+#!/bin/bash
+
+# RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)"
+RUN_ID="scglue"
+resources_dir="s3://openproblems-data/resources/grn"
+publish_dir="s3://openproblems-data/resources/grn/results/${RUN_ID}"
+
+
+param_file="./params/${RUN_ID}.yaml"
+
+cat > $param_file << HERE
+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}/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_inference.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