feat: json schema

Snakefile

@@ -22,7 +22,6 @@ _config.init_global(config)
 
 out_dir = _config.config.out_dir
 algorithm_params = _config.config.algorithm_params
-algorithm_directed = _config.config.algorithm_directed
 pca_params = _config.config.pca_params
 hac_params = _config.config.hac_params
 container_settings = _config.config.container_settings
@@ -273,16 +272,12 @@ rule reconstruct:
     run:
         # Create a copy so that the updates are not written to the parameters logfile
         params = reconstruction_params(wildcards.algorithm, wildcards.params).copy()
-        # Add the input files
-        params.update(dict(zip(runner.get_required_inputs(wildcards.algorithm), *{input}, strict=True)))
-        # Add the output file
-        # All run functions can accept a relative path to the output file that should be written that is called 'output_file'
-        params['output_file'] = output.pathway_file
-        # Remove the default placeholder parameter added for algorithms that have no parameters
-        if 'spras_placeholder' in params:
-            params.pop('spras_placeholder')
-        params['container_settings'] = container_settings
-        runner.run(wildcards.algorithm, params)
+        # Declare the input files as a dictionary.
+        inputs = dict(zip(runner.get_required_inputs(wildcards.algorithm), *{input}, strict=True))
+        # Remove the _spras_run_name parameter added for keeping track of the run name for parameters.yml
+        if '_spras_run_name' in params:
+            params.pop('_spras_run_name')
+        runner.run(wildcards.algorithm, inputs, output.pathway_file, params, container_settings)
 
 # Original pathway reconstruction output to universal output
 # Use PRRunner as a wrapper to call the algorithm-specific parse_output

config/config.yaml

@@ -1,8 +1,12 @@
+# Specify the schema:
+# yaml-language-server: $schema=schema.json
+
 # Global workflow control
 
 # The length of the hash used to identify a parameter combination
 hash_length: 7
 
+# Collection of container options
 containers:
   # Specify the container framework used by each PRM wrapper. Valid options include:
   # - docker (default if not specified)
@@ -60,23 +64,23 @@ containers:
 
 algorithms:
   - name: "pathlinker"
-    params:
-      include: true
+    include: true
+    runs:
       run1:
         k: range(100,201,100)
 
   - name: "omicsintegrator1"
-    params:
-      include: true
+    include: true
+    runs:
       run1:
         b: [5, 6]
         w: np.linspace(0,5,2)
         d: 10
         dummy_mode: "file" # Or "terminals", "all", "others"
 
   - name: "omicsintegrator2"
-    params:
-      include: true
+    include: true
+    runs:
       run1:
         b: 4
         g: 0
@@ -85,52 +89,50 @@ algorithms:
         g: 3
 
   - name: "meo"
-    params:
-      include: true
+    include: true
+    runs:
       run1:
         max_path_length: 3
-        local_search: "Yes"
+        local_search: true
         rand_restarts: 10
 
   - name: "mincostflow"
-    params:
-      include: true
+    include: true
+    runs:
       run1:
-        flow: 1 # The flow must be an int
+        flow: 1
         capacity: 1
 
   - name: "allpairs"
-    params:
-      include: true
+    include: true
 
   - name: "domino"
-    params:
-      include: true
+    include: true
+    runs:
       run1:
         slice_threshold: 0.3
         module_threshold: 0.05
 
   - name: "strwr"
-    params:
-      include: true
+    include: true
+    runs:
       run1:
         alpha: [0.85]
         threshold: [100, 200]
 
   - name: "rwr"
-    params:
-      include: true
+    include: true
+    runs:
       run1:
         alpha: [0.85]
         threshold: [100, 200]
 
   - name: "bowtiebuilder"
-    params:
-      include: true
+    include: true
 
   - name: "responsenet"
-    params:
-      include: true
+    include: true
+    runs:
       run1:
         gamma: [10]
 

config/egfr.yaml

@@ -1,4 +1,3 @@
-# The length of the hash used to identify a parameter combination
 hash_length: 7
 
 containers:
@@ -29,108 +28,83 @@ containers:
 
 algorithms:
   - name: pathlinker
-    params:
-      include: true
+    include: true
+    runs:
       run1:
         k:
           - 10
           - 20
           - 70
   - name: omicsintegrator1
-    params:
-      include: true
+    include: true
+    runs:
       run1:
         b:
           - 0.55
           - 2
           - 10
-        d:
-          - 10
-        g:
-          - 1e-3
-        r:
-          - 0.01
-        w:
-          - 0.1
-        mu:
-          - 0.008
+        d: 10
+        g: 1e-3
+        r: 0.01
+        w: 0.1
+        mu: 0.008
         dummy_mode: ["file"]
   - name: omicsintegrator2
-    params:
-      include: true
+    include: true
+    runs:
       run1:
-        b:
-          - 4
-        g:
-          - 0
+        b: 4
+        g: 0
       run2:
-        b:
-          - 2
-        g:
-          - 3
+        b: 2
+        g: 3
   - name: meo
-    params:
-      include: true
+    include: true
+    runs:
       run1:
-        local_search:
-          - "Yes"
-        max_path_length:
-          - 3
-        rand_restarts:
-          - 10
+        local_search: true
+        max_path_length: 3
+        rand_restarts: 10
       run2:
-        local_search:
-          - "No"
-        max_path_length:
-          - 2
-        rand_restarts:
-          - 10
+        local_search: false
+        max_path_length: 2
+        rand_restarts: 10
   - name: allpairs
-    params:
-      include: true
+    include: true
   - name: domino
-    params:
-      include: true
+    include: true
+    runs:
       run1:
-        slice_threshold:
-          - 0.3
-        module_threshold:
-          - 0.05
+        slice_threshold: 0.3
+        module_threshold: 0.05
   - name: mincostflow
-    params:
-      include: true
+    include: true
+    runs:
       run1:
-        capacity:
-          - 15
-        flow:
-          - 80
+        capacity: 15
+        flow: 80
       run2:
-        capacity:
-          - 1
-        flow:
-          - 6
+        capacity: 1
+        flow: 6
       run3:
-        capacity:
-          - 5
-        flow:
-          - 60
+        capacity: 5
+        flow: 60
   - name: "strwr"
-    params:
-      include: true
+    include: true
+    runs:
       run1:
         alpha: [0.85]
         threshold: [100, 200]
 
   - name: "rwr"
-    params:
-      include: true
+    include: true
+    runs:
       run1:
         alpha: [0.85]
         threshold: [100, 200]
 
   - name: "bowtiebuilder"
-    params:
-      include: false
+    include: false
 datasets:
   - data_dir: input
     edge_files: