removed directed from config file, testing with analysis all false

config/config.yaml

@@ -29,14 +29,12 @@
         - name: "pathlinker"
           params:
                 include: true
-                directed: true
                 run1:
                     k: range(100,201,100)
 
         - name: "omicsintegrator1"
           params:
                 include: true
-                directed: false
                 run1:
                     r: [5]
                     b: [5, 6]
@@ -47,7 +45,6 @@
         - name: "omicsintegrator2"
           params:
                 include: true
-                directed: false
                 run1:
                     b: [4]
                     g: [0]
@@ -58,7 +55,6 @@
         - name: "meo"
           params:
                 include: true
-                directed: true
                 run1:
                     max_path_length: [3]
                     local_search: ["Yes"]
@@ -67,20 +63,17 @@
         - name: "mincostflow"
           params:
                 include: true
-                directed: false
                 run1:
                     flow: [1] # The flow must be an int
                     capacity: [1]
 
         - name: "allpairs"
           params:
                 include: true
-                directed: false
 
         - name: "domino"
           params:
                 include: true
-                directed: false
                 run1:
                     slice_threshold: [0.3]
                     module_threshold: [0.05]
@@ -125,13 +118,13 @@
  analysis:
         # Create one summary per pathway file and a single summary table for all pathways for each dataset
         summary:
-          include: true
+          include: false
         # Create output files for each pathway that can be visualized with GraphSpace
         graphspace:
-          include: true
+          include: false
         # Machine learning analysis (e.g. clustering) of the pathway output files for each dataset
         ml:
-          include: true
+          include: false
           # specify how many principal components to calculate
           components: 2
           # boolean to show the labels on the pca graph

src/util.py

@@ -313,9 +313,6 @@ def process_config(config):
             # Do not parse the rest of the parameters for this algorithm if it is not included
             continue
 
-        if "directed" in cur_params:
-            algorithm_directed[alg["name"]] = cur_params.pop("directed")
-
         # The algorithm has no named arguments so create a default placeholder
         if len(cur_params) == 0:
             cur_params["run1"] = {"spras_placeholder": ["no parameters"]}