Write one Cytoscape session per dataset

Snakefile

@@ -70,7 +70,7 @@ def make_final_input(wildcards):
         final_input.extend(expand('{out_dir}{sep}{dataset}-{algorithm_params}{sep}gsstyle.json',out_dir=out_dir,sep=SEP,dataset=dataset_labels,algorithm_params=algorithms_with_params))
 
     if config["analysis"]["cytoscape"]["include"]:
-        final_input.extend(expand('{out_dir}{sep}cytoscape-session.cys',out_dir=out_dir,sep=SEP))
+        final_input.extend(expand('{out_dir}{sep}{dataset}-cytoscape.cys',out_dir=out_dir,sep=SEP,dataset=dataset_labels))
 
     if config["analysis"]["ml"]["include"]:  
         final_input.extend(expand('{out_dir}{sep}{dataset}-pca.png',out_dir=out_dir,sep=SEP,dataset=dataset_labels,algorithm_params=algorithms_with_params))
@@ -238,13 +238,13 @@ rule viz_graphspace:
         graphspace.write_json(input.standardized_file,output.graph_json,output.style_json,directed=algorithm_directed[wildcards.algorithm])
 
 
-# Write Cytoscape session file with all pathways for all datasets
+# Write a Cytoscape session file with all pathways for each dataset
 rule viz_cytoscape:
-    input: pathways = expand('{out_dir}{sep}{dataset}-{algorithm_params}{sep}pathway.txt', out_dir=out_dir, sep=SEP, dataset=dataset_labels, algorithm_params=algorithms_with_params)
+    input: pathways = expand('{out_dir}{sep}{{dataset}}-{algorithm_params}{sep}pathway.txt', out_dir=out_dir, sep=SEP, algorithm_params=algorithms_with_params)
     output: 
-        session = SEP.join([out_dir, 'cytoscape-session.cys'])
+        session = SEP.join([out_dir, '{dataset}-cytoscape.cys'])
     run:
-        cytoscape.run_cytoscape_container(input.pathways, out_dir, SINGULARITY)
+        cytoscape.run_cytoscape_container(input.pathways, output.session, SINGULARITY)
 
 
 # Write a single summary table for all pathways for each dataset

docker-wrappers/Cytoscape/cytoscape_util.py

@@ -1,5 +1,4 @@
 import argparse
-import os
 import subprocess
 import time
 from typing import List
@@ -29,19 +28,12 @@ def get_parser() -> argparse.ArgumentParser:
     )
 
     parser.add_argument(
-        "--outdir",
-        dest='outdir',
+        "--output",
+        dest='output',
         type=str,
-        default='output',
-        help='The output directory of the session file. Default: output'
-    )
-
-    parser.add_argument(
-        "--outlabel",
-        dest='outlabel',
-        type=str,
-        default='cytoscape-session',
-        help='The output filename of the session file, which will have the extension .cys. Default: cytoscape-session'
+        default='cytoscape-session.cys',
+        help='The output filename of the Cytoscape session file, which will have the extension .cys added if it is not '
+             'already provided. Default: cytoscape-session.cys'
     )
     return parser
 
@@ -99,7 +91,7 @@ def parse_name(pathway: str) -> (str, str):
         return parts[0], parts[1]
 
 
-def load_pathways(pathways: List[str], out_dir: str, out_label: str) -> None:
+def load_pathways(pathways: List[str], output: str) -> None:
     if len(pathways) == 0:
         raise ValueError('One or more pathway files are required')
 
@@ -113,12 +105,12 @@ def load_pathways(pathways: List[str], out_dir: str, out_label: str) -> None:
         )
         p4c.networks.rename_network(name, network=suid)
 
-    p4c.session.save_session(os.path.join(out_dir, out_label))
+    p4c.session.save_session(output)
 
 
 def main():
     opts = parse_arguments()
-    load_pathways(opts.pathways, opts.outdir, opts.outlabel)
+    load_pathways(opts.pathways, opts.output)
 
 
 if __name__ == '__main__':

src/analysis/cytoscape.py

@@ -5,7 +5,7 @@
 from src.util import prepare_volume, run_container
 
 
-def run_cytoscape_container(pathways: List[Union[str, PurePath]], out_dir: str, singularity: bool = False) -> None:
+def run_cytoscape_container(pathways: List[Union[str, PurePath]], output_file: str, singularity: bool = False) -> None:
     """
     1. take pathways and create volume mappings
     2. setup wrapper command
@@ -21,7 +21,8 @@ def run_cytoscape_container(pathways: List[Union[str, PurePath]], out_dir: str,
     # Each volume is a tuple (src, dest)
     volumes = list()
 
-    cytoscape_output_dir = Path(out_dir, 'cytoscape').absolute()
+    # A temporary directory for Cytoscape output files
+    cytoscape_output_dir = Path(output_file.replace('.cys', '')).absolute()
     cytoscape_output_dir.mkdir(parents=True, exist_ok=True)
 
     # TODO update the latest p4cytoscape and use env variable to control the log directory instead
@@ -30,14 +31,12 @@ def run_cytoscape_container(pathways: List[Union[str, PurePath]], out_dir: str,
     # Only needed when running in Singularity
     volumes.append((cytoscape_output_dir, PurePath(work_dir, 'CytoscapeConfiguration')))
 
-    # Map the output directory
-    bind_path, mapped_out_dir = prepare_volume(out_dir, work_dir)
+    # Map the output file
+    bind_path, mapped_output = prepare_volume(output_file, work_dir)
     volumes.append(bind_path)
 
-    # Create the Python command to run inside the container
-    command = ['python', '/py4cytoscape/cytoscape_util.py',
-               '--outdir', mapped_out_dir,
-               '--outlabel', 'cytoscape-session']
+    # Create the initial Python command to run inside the container
+    command = ['python', '/py4cytoscape/cytoscape_util.py', '--output', mapped_output]
 
     # Map the pathway filenames and add them to the Python command
     for pathway in pathways: