From 9aeb7b811eb0a3c5f339f40348fb02ecb48b0167 Mon Sep 17 00:00:00 2001 From: james hadfield Date: Mon, 9 Dec 2024 11:54:39 +1300 Subject: [PATCH] WIP shift cattle-outbreak custom rule Allows config overlays to use custom-rules without needing to also add the "cattle-flu.smk" entry. --- h5n1-cattle-outbreak/Snakefile | 2 ++ {rules => h5n1-cattle-outbreak}/cattle-flu.smk | 0 h5n1-cattle-outbreak/config.yaml | 9 --------- 3 files changed, 2 insertions(+), 9 deletions(-) rename {rules => h5n1-cattle-outbreak}/cattle-flu.smk (100%) 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 2432a7f..897f74f 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: ''