WIP shift cattle-outbreak custom rule

Allows config overlays to use custom-rules without needing to also add the "cattle-flu.smk" entry.
nextstrain · Dec 8, 2024 · 9aeb7b8 · 9aeb7b8
1 parent a519284
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diff --git 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
diff --git a/rules/cattle-flu.smk → h5n1-cattle-outbreak/cattle-flu.smk b/rules/cattle-flu.smk → h5n1-cattle-outbreak/cattle-flu.smk
diff --git 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: ''