bug in scenic fixed

openproblems-bio · Sep 15, 2024 · d9e1ef0 · d9e1ef0
1 parent ba16d85
commit d9e1ef0
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Showing 4 changed files with 6 additions and 33 deletions.
diff --git a/src/methods/single_omics/pidc/config.vsh.yaml b/src/methods/single_omics/pidc/config.vsh.yaml
@@ -1,3 +1,5 @@
+__merge__: ../../../api/comp_method.yaml
+
 functionality:
   name: pidc
   info:
@@ -6,35 +8,7 @@ functionality:
     description: |
       GRN inference using PIDC.
     documentation_url: https://rdrr.io/github/hmutpw/PIDC/
-  arguments:
-    - name: --multiomics_rna
-      type: file
-      example: resources/grn-benchmark/multiomics_rna.h5ad
-      info:
-        label: multiomics_rna
-        summary: "Multiomics RNA data"
-        file_type: rds
-        columns: 
-          - name: dummpy
-            type: string
-            required: false
-      required: true
-      must_exist: true
-    - name: --prediction
-      __merge__: ../../api/file_prediction.yaml
-      required: true
-      direction: output
-    - name: --max_n_links
-      type: integer
-      default: 50000
-    - name: --temp_dir
-      type: file
-      direction: output
-      default: 'output/pidc'
-    - name: --num_workers
-      type: integer
-      direction: input
-      default: 4
+
   resources:
     - type: python_script
       path: script.py

diff --git a/src/methods/single_omics/scenic/config.vsh.yaml b/src/methods/single_omics/scenic/config.vsh.yaml
@@ -14,12 +14,12 @@ functionality:
       required: false
       default: 5000 
     - name: --auc_threshold
-      type: float
+      type: double
       direction: input 
       required: false
       default: 0.05 
     - name: --nes_threshold
-      type: float
+      type: double
       direction: input 
       required: false
       default: 3.0

diff --git a/src/workflows/run_benchmark_single_omics/config.vsh.yaml b/src/workflows/run_benchmark_single_omics/config.vsh.yaml
@@ -88,7 +88,7 @@ functionality:
     - name: grn_methods/ennet
     - name: grn_methods/genie3
     - name: grn_methods/grnboost2
-    - name: grn_methods/pidc
+    # - name: grn_methods/pidc
     - name: grn_methods/ppcor
     - name: grn_methods/scsgl
     - name: grn_methods/tigress

diff --git a/src/workflows/run_benchmark_single_omics/main.nf b/src/workflows/run_benchmark_single_omics/main.nf
@@ -17,7 +17,6 @@ workflow run_wf {
     ennet,
     genie3,
     grnboost2,
-    pidc,
     ppcor,
     scsgl,
     tigress,
-Original file line number
+Diff line change
@@ Expand Up / @@ -17,7 +17,6 @@ workflow run_wf { @@
         ennet,
         genie3,
         grnboost2,
-        pidc,
         ppcor,
         scsgl,
         tigress,
@@ Expand Down @@