From f3b23e065ba6fb665f87dcd7c523a7d9428addd9 Mon Sep 17 00:00:00 2001 From: "@rvosa" Date: Sun, 21 Apr 2024 19:02:45 +0200 Subject: [PATCH] entire odonate pipeline runs --- workflow/Snakefile | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/workflow/Snakefile b/workflow/Snakefile index 3e5e3ab..0e6ab69 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -377,7 +377,11 @@ rule run_raxml_backbone: --search > {log} 2>&1 """ - +# Reroots the backbone using the constraint tree. The basic method is to find the +# basal split in the constraint, look for the equivalent bipartition in the inferred +# tree, and root there. TODO: this approach currently places the root on the midpoint +# of the bipartition. This is not ideal but it is not obvious what better options +# are available if there are no outgroups. rule reroot_backbone: input: backbone = "results/fasta/raxml-ready.fa.raxml.bestTree", @@ -401,7 +405,8 @@ rule reroot_backbone: rule graft_clades: input: backbone = "results/fasta/raxml-ready.fa.raxml.bestTree.rooted", - clades = config['file_names']['fasta_dir'] + clades = config['file_names']['fasta_dir'], + extinct = "results/fasta/extinct_pids.txt" output: tree = "results/grafted.tre" params: @@ -414,6 +419,7 @@ rule graft_clades: python workflow/scripts/graft_clades.py \ -t {input.backbone} \ -f {input.clades} \ + -e {input.extinct} \ -o {output.tree} \ -n {params.nfamilies} \ -v {params.log_level} 2> {log}