WIP remove cattle-outbreak custom rule

Shifts to a concept where custom-rules are only for use in analysis
directories, and the custom snakemake file is sourced relative to that
working directory. See <#103 (comment)>
for more discussion about the benefits and limitations of this.

The cattle-outbreak workflow (`h5n1-cattle-outbreak/Snakefile`) now
directly imports the rules it needs rather than using the custom-rules
machinery.

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)

h5n1-cattle-outbreak/Snakefile

@@ -1,4 +1,6 @@
 include: "../Snakefile"
 
+include: "cattle-flu.smk"
+
 rule _all:
     input: rules.all.input

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: ''