From 1e8e98d20310d6223f22bdf35949133a3f9b2429 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Wed, 27 Mar 2024 08:39:29 +0000 Subject: [PATCH] phylo: Update config section of README to reflect reality Copied commit from zika: https://github.com/nextstrain/zika/pull/51/commits/810e1d217bc8de7bd233f426a498abbc3bba5e8a As duplicating https://github.com/nextstrain/zika/pull/51 --- phylogenetic/README.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/phylogenetic/README.md b/phylogenetic/README.md index 0636e776..119928fd 100644 --- a/phylogenetic/README.md +++ b/phylogenetic/README.md @@ -27,9 +27,10 @@ Once you've run the build, you can view the results in auspice: ## Configuration -Configuration takes place entirely with the `Snakefile`. This can be read top-to-bottom, each rule -specifies its file inputs and output and also its parameters. There is little redirection and each -rule should be able to be reasoned with on its own. +Configuration for the workflow takes place entirely within the [defaults/config_dengue.ymal](defaults/config_dengue.yaml). +The analysis pipeline is contained in [Snakefile](Snakefile) with included [rules](rules). +Each rule specifies its file inputs and output and pulls its parameters from the config. +There is little redirection and each rule should be able to be reasoned with on its own. ### Using GenBank data