run grn pipeline updated

openproblems-bio · Jan 23, 2025 · 3147fb2 · 3147fb2
1 parent 5e2bfea
commit 3147fb2
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Showing 9 changed files with 14 additions and 2 deletions.
diff --git a/scripts/run_benchmark_all.sh b/scripts/run_benchmark_all.sh
@@ -52,7 +52,7 @@ HERE
 #     --params-file ./params/benchmark_donor_0_default.yaml `
 #     --config src/common/nextflow_helpers/labels_tw.config
 
-./tw launch https://github.com/openproblems-bio/task_grn_inference \
+tw launch https://github.com/openproblems-bio/task_grn_inference \
   --revision build/main \
   --pull-latest \
   --main-script target/nextflow/workflows/run_benchmark/main.nf \

diff --git a/scripts/run_grn_evaluation.sh b/scripts/run_grn_evaluation.sh
@@ -64,7 +64,10 @@ append_entry() {
     num_workers: $num_workers
     tf_all: ${resources_dir}/prior/tf_all.csv
     regulators_consensus: ${resources_dir}/prior/regulators_consensus_${dataset}.json
+    ws_consensus: ${resources_dir}/prior/ws_consensus_${dataset}.json
+    ws_distance_background: ${resources_dir}/prior/ws_distance_background_${dataset}.json
     prediction: ${grn_models_folder}/${dataset}/$1.csv
+    layer: "X_norm"
 HERE
 }
 

diff --git a/..._analysis/gene_annotation/config.vsh.yaml → ...nalysis/gene_annotation/config.novsh.yaml b/..._analysis/gene_annotation/config.vsh.yaml → ...nalysis/gene_annotation/config.novsh.yaml
diff --git a/...ta/multiomics/format_data/config.vsh.yaml → .../multiomics/format_data/config.novsh.yaml b/...ta/multiomics/format_data/config.vsh.yaml → .../multiomics/format_data/config.novsh.yaml
diff --git a/...s_data/perturbation/opsca/config.vsh.yaml → ...data/perturbation/opsca/config.novsh.yaml b/...s_data/perturbation/opsca/config.vsh.yaml → ...data/perturbation/opsca/config.novsh.yaml
diff --git a/...kflows/process_multiomics/config.vsh.yaml → ...lows/process_multiomics/config.novsh.yaml b/...kflows/process_multiomics/config.vsh.yaml → ...lows/process_multiomics/config.novsh.yaml
diff --git a/...lows/process_perturbation/config.vsh.yaml → ...ws/process_perturbation/config.novsh.yaml b/...lows/process_perturbation/config.vsh.yaml → ...ws/process_perturbation/config.novsh.yaml
diff --git a/src/workflows/run_grn_evaluation/config.vsh.yaml b/src/workflows/run_grn_evaluation/config.vsh.yaml
@@ -13,6 +13,14 @@ functionality:
           type: file
           required: true
           direction: input
+        - name: --prediction
+          type: file
+          required: true
+          direction: input
+        - name: --layer
+          type: string
+          required: true
+          direction: input
         - name: --method_id
           type: string
           required: true

diff --git a/src/workflows/run_grn_evaluation/main.nf b/src/workflows/run_grn_evaluation/main.nf
@@ -13,7 +13,7 @@ workflow run_wf {
   main:
 
   // construct list of metrics
-  metrics_regression = [
+  metrics = [
     regression_1,
     regression_2
   ]
@@ -61,6 +61,7 @@ workflow run_wf {
         method_id: "method_id",
         num_workers: "num_workers",
         regulators_consensus: "regulators_consensus",
+        ws_consensus: "ws_consensus",
         layer: "layer",
         tf_all: "tf_all"
       ],