bug in run benchmark single omics fixed

openproblems-bio · Sep 5, 2024 · 63b40d5 · 63b40d5
1 parent a255f91
commit 63b40d5
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Showing 5 changed files with 34 additions and 27 deletions.
diff --git a/scripts/run_benchmark_single_omics.sh b/scripts/run_benchmark_single_omics.sh
@@ -1,16 +1,17 @@
 #!/bin/bash
 
 # RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)"
-RUN_ID="single_omics_test"
-# resources_dir="s3://openproblems-data/resources_test/grn"
-# publish_dir="s3://openproblems-data/resources_test/grn/results/${RUN_ID}"
+RUN_ID="single_omics_all_test"
+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/${RUN_ID}"
+# resources_dir="./resources_test/"
+# publish_dir="output/${RUN_ID}"
 
 reg_type=ridge
 subsample=-2
 max_workers=10
+layer='pearson'
 
 param_file="./params/${RUN_ID}.yaml"
 
@@ -23,6 +24,7 @@ param_list:
     reg_type: $reg_type
     subsample: $subsample
     max_workers: $max_workers
+    layer: $layer
     consensus: ${resources_dir}/prior/consensus-num-regulators.json
     tf_all: ${resources_dir}/prior/tf_all.csv
 output_state: "state.yaml"
@@ -36,14 +38,14 @@ nextflow run . \
   -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/scgen_pearson_gb_pcs.yaml `
-#     --config src/common/nextflow_helpers/labels_tw.config
+./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_benchmark_single_omics/main.nf `
+    --workspace 53907369739130 `
+    --compute-env 6TeIFgV5OY4pJCk8I0bfOh `
+    --params-file ./params/single_omics_all_test.yaml `
+    --config src/common/nextflow_helpers/labels_tw.config
 
 
diff --git a/src/methods/multi_omics/scenicplus/script.py b/src/methods/multi_omics/scenicplus/script.py
@@ -584,8 +584,8 @@
 ###############################################################################################
 ###############################################################################################
 
-RANKINGS_DB_PATH = os.path.join(out_dir, 'cistarget-db', 'db', 'db.regions_vs_motifs.rankings.feather')
-SCORES_DB_PATH = os.path.join(out_dir, 'cistarget-db', 'db', 'db.regions_vs_motifs.scores.feather')
+RANKINGS_DB_PATH = os.path.join(out_dir, 'cistarget-db', 'db.regions_vs_motifs.rankings.feather')
+SCORES_DB_PATH = os.path.join(out_dir, 'cistarget-db', 'db.regions_vs_motifs.scores.feather')
 
 if not (os.path.exists(RANKINGS_DB_PATH) and os.path.exists(SCORES_DB_PATH)):
 

diff --git a/src/methods/multi_omics/scglue_ns/run.sh b/src/methods/multi_omics/scglue_ns/run.sh
@@ -5,7 +5,6 @@ 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"
 
@@ -24,12 +23,12 @@ 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
+# ./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
diff --git a/src/workflows/run_benchmark_single_omics/config.vsh.yaml b/src/workflows/run_benchmark_single_omics/config.vsh.yaml
@@ -44,6 +44,11 @@ functionality:
           required: false
           direction: input
           default: resources/prior/consensus.json
+        - name: --layer
+          type: string
+          required: false
+          direction: input
+          default: pearson
 
     - name: Outputs
       arguments:

diff --git a/src/workflows/run_benchmark_single_omics/main.nf b/src/workflows/run_benchmark_single_omics/main.nf
@@ -106,7 +106,8 @@ workflow run_wf {
         reg_type: "reg_type",
         max_workers: "max_workers",
         consensus: "consensus",
-        tf_all: "tf_all"
+        tf_all: "tf_all",
+        layer:"layer"
       ],
       // use 'toState' to publish that component's outputs to the overall state
       toState: { id, output, state, comp ->