From b7fc4533ba44b5c0accc597525edbf8056320d18 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Mon, 3 Jun 2024 16:11:42 -0700 Subject: [PATCH] Infer ancestral root This commit reverts the change introduced in https://github.com/nextstrain/dengue/pull/57/commits/94316551c8af6270134411305098a0694eb17811 which set the REFSEQ references as the roots in the auspice trees. Turns out this is not the desired behavior for the dengue phylogenetic trees. Instead, we want to use the sequences and metadata to infer the ancestral root of each tree. These inferred-ancestral roots will then be used in building the nextclade datasets as hard-coded reference and root of the scaffold trees. --- phylogenetic/rules/annotate_phylogeny.smk | 2 -- 1 file changed, 2 deletions(-) diff --git a/phylogenetic/rules/annotate_phylogeny.smk b/phylogenetic/rules/annotate_phylogeny.smk index 2eb89284..4e3338e4 100644 --- a/phylogenetic/rules/annotate_phylogeny.smk +++ b/phylogenetic/rules/annotate_phylogeny.smk @@ -26,7 +26,6 @@ rule ancestral: input: tree = "results/{gene}/tree_{serotype}.nwk", alignment = "results/{gene}/aligned_{serotype}.fasta", - root_sequence = lambda wildcard: "config/reference_{serotype}_genome.gb" if wildcard.gene in ['genome'] else "results/config/reference_{serotype}_{gene}.gb", output: node_data = "results/{gene}/nt-muts_{serotype}.json" params: @@ -37,7 +36,6 @@ rule ancestral: --tree {input.tree} \ --alignment {input.alignment} \ --output-node-data {output.node_data} \ - --root-sequence {input.root_sequence} \ --inference {params.inference} """