diff --git a/Snakefile b/Snakefile
index 1d36448..c91d7ad 100755
--- a/Snakefile
+++ b/Snakefile
@@ -732,4 +732,5 @@ rule clean:
 
 
 for rule_file in config.get('custom_rules', []):
-    include: rule_file
+    # Relative custom rule paths in the config are expected to be relative to the analysis (working) directory
+    include: os.path.join(os.getcwd(), rule_file)
diff --git a/h5n1-cattle-outbreak/Snakefile b/h5n1-cattle-outbreak/Snakefile
index d5db20f..3433d5d 100644
--- a/h5n1-cattle-outbreak/Snakefile
+++ b/h5n1-cattle-outbreak/Snakefile
@@ -1,4 +1,6 @@
 include: "../Snakefile"
 
+include: "cattle-flu.smk"
+
 rule _all:
     input: rules.all.input
\ No newline at end of file
diff --git a/rules/cattle-flu.smk b/h5n1-cattle-outbreak/cattle-flu.smk
similarity index 100%
rename from rules/cattle-flu.smk
rename to h5n1-cattle-outbreak/cattle-flu.smk
diff --git a/h5n1-cattle-outbreak/config.yaml b/h5n1-cattle-outbreak/config.yaml
index 6a962d7..3be1b69 100644
--- a/h5n1-cattle-outbreak/config.yaml
+++ b/h5n1-cattle-outbreak/config.yaml
@@ -1,12 +1,3 @@
-# NOTE: The h5n1-cattle-outbreak builds use a specific rule-file (specified within this config)
-# and that rule file may have some config-like parameters within it.
-# If you are extending this workflow via a --configfile overlay you and you want to add
-# your own custom rule you will need to include "rules/cattle-flu.smk" as an element in the
-# list in your overlay, as lists are not merged when configs are combined.
-custom_rules:
-  - "rules/cattle-flu.smk"
-
-
 #### Parameters which define which builds to produce via this config ###
 builds:
   h5n1-cattle-outbreak: ''