diff --git a/nextclade/defaults/auspice_config.json b/nextclade/defaults/auspice_config.json index 07109d8..9f6c685 100644 --- a/nextclade/defaults/auspice_config.json +++ b/nextclade/defaults/auspice_config.json @@ -11,11 +11,6 @@ "title": "Genotype", "type": "categorical" }, - { - "key": "num_date", - "title": "Date", - "type": "continuous" - }, { "key": "clade_membership", "title": "MeV Genotype (Nextstrain)", diff --git a/nextclade/rules/construct_phylogeny.smk b/nextclade/rules/construct_phylogeny.smk index 5a34b9e..45a1554 100644 --- a/nextclade/rules/construct_phylogeny.smk +++ b/nextclade/rules/construct_phylogeny.smk @@ -31,7 +31,6 @@ rule refine: metadata = "data/metadata.tsv" output: tree = "results/tree.nwk", - node_data = "results/branch_lengths.json" params: coalescent = config["refine"]["coalescent"], date_inference = config["refine"]["date_inference"], @@ -45,7 +44,6 @@ rule refine: --metadata {input.metadata} \ --metadata-id-columns {params.strain_id} \ --output-tree {output.tree} \ - --output-node-data {output.node_data} \ --timetree \ --coalescent {params.coalescent} \ --date-confidence \ diff --git a/nextclade/rules/export.smk b/nextclade/rules/export.smk index 45ac446..894622a 100644 --- a/nextclade/rules/export.smk +++ b/nextclade/rules/export.smk @@ -10,7 +10,6 @@ rule export: input: tree = "results/tree.nwk", metadata = "data/metadata.tsv", - branch_lengths = "results/branch_lengths.json", clades = "results/clades.json", nt_muts = "results/nt_muts.json", aa_muts = "results/aa_muts.json", @@ -27,7 +26,7 @@ rule export: --tree {input.tree} \ --metadata {input.metadata} \ --metadata-id-columns {params.strain_id} \ - --node-data {input.branch_lengths} {input.nt_muts} {input.aa_muts} {input.clades} \ + --node-data {input.nt_muts} {input.aa_muts} {input.clades} \ --colors {input.colors} \ --metadata-columns {params.metadata_columns} \ --auspice-config {input.auspice_config} \