robust analysis fixed

scripts/run_robust_analys.sh

@@ -3,10 +3,15 @@
 # RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)"
 
 RUN_ID="robust_analy"
-resources_dir="resources"
-publish_dir="output/${RUN_ID}"
+# resources_dir="resources"
+# publish_dir="output/${RUN_ID}"
+
+resources_dir="s3://openproblems-data/resources/grn"
+publish_dir="s3://openproblems-data/resources/grn/results/${RUN_ID}"
 
 grn_models_folder="${resources_dir}/grn_models"
+
+
 reg_type=ridge
 subsample=-2
 max_workers=10
@@ -35,6 +40,7 @@ HERE
 append_entry() {
   cat >> $param_file << HERE
   - id: ${1}_${2}_${3}
+    perturbation_data: ${resources_dir}/grn-benchmark/perturbation_data.h5ad
     layer: ${layer}
     reg_type: $reg_type
     method_id: $1

src/methods/multi_omics/scenicplus/config.vsh.yaml

@@ -3,6 +3,7 @@ __merge__: ../../../api/comp_method.yaml
 
 functionality:
   name: scenicplus
+  namespace: grn_methods
   info:
     label: scenicplus
     summary: "GRN inference using scenicplus"

src/methods/multi_omics/scenicplus_ns/config.vsh.yaml

@@ -0,0 +1,21 @@
+
+__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."
+
+  resources:
+    - type: nextflow_script
+      path: main.nf
+      entrypoint: run_wf
+  dependencies:
+    - name: grn_methods/scenicplus 
+
+platforms:
+  - type: nextflow
+    directives:
+      label: [ midtime, midmem, lowcpu ]

src/methods/multi_omics/scenicplus_ns/main.nf

@@ -0,0 +1,21 @@
+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"]
+    )
+
+    | setState(["prediction"])
+
+  emit:
+  output_ch
+}

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=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
+
+
+# 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_benchmark.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
+
+

src/workflows/run_robustness_analysis/config.vsh.yaml

@@ -1,4 +1,3 @@
-
 functionality:
   name: run_robustness_analysis
   namespace: "workflows"
@@ -8,6 +7,9 @@ functionality:
   argument_groups:
     - name: Inputs
       arguments:
+        - name: --perturbation_data
+          type: file
+          direction: input
         - name: --layer
           type: string
           direction: input

src/workflows/run_robustness_analysis/main.nf

@@ -42,6 +42,7 @@ workflow run_wf {
       },
       // use 'fromState' to fetch the arguments the component requires from the overall state
       fromState: [
+        perturbation_data: "perturbation_data",
         prediction_n: "prediction",
         layer: "layer", 
         subsample: "subsample",