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Put params in order of use [#2]
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genehack committed Nov 20, 2024
1 parent 8f9dc75 commit 5c62c7c
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion phylogenetic/rules/construct_phylogeny.smk
Original file line number Diff line number Diff line change
Expand Up @@ -35,13 +35,13 @@ rule refine:
tree = "results/{gene}/tree.nwk",
node_data = "results/{gene}/branch_lengths.json"
params:
strain_id = config["strain_id_field"],
timetree = lambda w: "--timetree" if w.gene == "genome" else "",
clock_rate = config["refine"]["clock_rate"],
clock_std_dev = config["refine"]["clock_std_dev"],
coalescent = config["refine"]["coalescent"],
date_inference = config["refine"]["date_inference"],
clock_filter_iqd = config["refine"]["clock_filter_iqd"],
strain_id = config["strain_id_field"]
log:
"logs/{gene}/refine.txt",
benchmark:
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