Add sh and cwl files to run aggregate_and_plot.py

aggregate_and_plot.cwl

+cwlVersion: v1.0
+class: CommandLineTool
+
+requirements:
+  - class: DockerRequirement
+    dockerPull: git.astron.nl:5000/ldv/imaging_compress_pipeline:v0.4.1
+
+baseCommand: python3
+arguments:
+  - /src/aggregate_and_plot.py
+
+inputs: {}
+
+outputs: []

aggregate_and_plot.py

@@ -9,7 +9,7 @@ logging.basicConfig(format=FORMAT, level="INFO")
 
 if __name__ == "__main__":
     h5_paths = []
-    with open("inputs.txt", "r") as file:
+    with open("/mnt/workdir/inputs.txt", "r") as file:
         for line in file:
             line = str(line.strip()) # remove white space
             path = Path(line)
@@ -23,11 +23,11 @@ if __name__ == "__main__":
                 logging.info(f"Could not find the following input file: {line}")
         logging.info(f"Found {len(h5_paths)} h5 files")
 
-    h5_output_path = "inspect.h5"
+    h5_output_path = "/mnt/workdir/inspect.h5"
     join_inspect_ds(h5_paths, h5_output_path)
-    plot_paths = plot_inspect_ds(h5_output_path, "./", min_elevation=15)
+    plot_paths = plot_inspect_ds(h5_output_path, "/mnt/workdir", min_elevation=15)
 
-    with open("outputs.txt", "w") as file:
+    with open("/mnt/workdir/outputs.txt", "w") as file:
         file.write(str(Path(h5_output_path).absolute()) + "\n")
         for file_path in plot_paths:
             path = Path(file_path).absolute()

aggregate_and_plot.sh

+#!/usr/bin/sh
+if [ -d "toil_venv" ]; then
+    echo "Activating existing virtual environment."
+    source toil_venv/bin/activate
+else
+    echo "Creating new virtual environment for using toil"
+    python3.11 -m venv toil_venv
+    source toil_venv/bin/activate
+    pip install --upgrade pip setuptools wheel
+    pip install toil[cwl] singularity
+fi
+export SINGULARITY_BIND="$PWD:/mnt/workdir,/project:/project"
+toil-cwl-runner --singularity imaging_compress_pipeline.git/aggregate_and_plot.cwl