Only assemble genome dataset

nextstrain · May 25, 2024 · d1fef70 · d1fef70
1 parent a249bf2
commit d1fef70
Show file tree

Hide file tree

Showing 3 changed files with 2 additions and 63 deletions.
diff --git a/nextclade/Snakefile b/nextclade/Snakefile
@@ -1,7 +1,7 @@
 configfile: "config/config_dengue.yaml"
 
 serotypes = ['all', 'denv1', 'denv2', 'denv3', 'denv4']
-genes = ['genome', 'E']
+genes = ['genome']
 
 wildcard_constraints:
     serotype = "|".join(serotypes),
@@ -14,7 +14,6 @@ rule all:
         test_dataset = expand("test_output/{serotype}", serotype=serotypes),
 
 include: "rules/prepare_sequences.smk"
-include: "rules/prepare_sequences_E.smk"
 include: "rules/construct_phylogeny.smk"
 include: "rules/annotate_phylogeny.smk"
 include: "rules/export.smk"

diff --git a/nextclade/rules/assemble_dataset.smk b/nextclade/rules/assemble_dataset.smk
@@ -13,7 +13,7 @@ See Augur's usage docs for these commands for more details.
 rule assemble_dataset:
     input:
         reference="resources/{serotype}/reference.fasta",
-        tree="auspice/dengue_{serotype}.json",
+        tree="auspice/dengue_{serotype}_genome.json",
         pathogen_json="resources/{serotype}/pathogen.json",
         #sequences="resources/{serotype}/sequences.fasta",
         annotation="resources/{serotype}/genome_annotation.gff3",

diff --git a/nextclade/rules/prepare_sequences_E.smk b/nextclade/rules/prepare_sequences_E.smk