Sync EGFR config file with general changes

Author: agitter

config/egfr.yaml

@@ -1,9 +1,28 @@
 # The length of the hash used to identify a parameter combination
 hash_length: 7
 
-# If true, use Singularity instead of Docker
-# Singularity support is only available on Unix
-singularity: false
+# Specify the container framework used by each PRM wrapper. Valid options include:
+# - docker (default if not specified)
+# - singularity -- Also known as apptainer, useful in HPC/HTC environments where docker isn't allowed
+# - dsub -- experimental with limited support, used for running on Google Cloud
+container_framework: docker
+
+# Only used if container_framework is set to singularity, this will unpack the singularity containers
+# to the local filesystem. This is useful when PRM containers need to run inside another container,
+# such as would be the case in an HTCondor/OSPool environment.
+# NOTE: This unpacks singularity containers to the local filesystem, which will take up space in a way
+# that persists after the workflow is complete. To clean up the unpacked containers, the user must
+# manually delete them.
+unpack_singularity: false
+
+# Allow the user to configure which container registry containers should be pulled from
+# Note that this assumes container names are consistent across registries, and that the
+# registry being passed doesn't require authentication for pull actions
+container_registry:
+  base_url: docker.io
+  # The owner or project of the registry
+  # For example, "reedcompbio" if the image is available as docker.io/reedcompbio/allpairs
+  owner: reedcompbio
 
 algorithms:
   - name: pathlinker
@@ -58,7 +77,7 @@ algorithms:
           - 10
       run2:
         local_search:
-          - 'No'
+          - "No"
         max_path_length:
           - 2
         rand_restarts:
@@ -112,8 +131,6 @@ reconstruction_settings:
     reconstruction_dir: output/egfr
   run: true
 analysis:
-  graphspace:
-    include: false
   cytoscape:
     include: true
   summary: