nextclade/export: Update REQUIRED INPUTS for Nextclade v3

Clarify the files required for `augur export` and the Nextclade v3 dataset files.
nextstrain · Oct 19, 2024 · ea71a78 · ea71a78
1 parent 22e8458
commit ea71a78
Showing 1 changed file with 15 additions and 13 deletions.
diff --git a/nextclade/rules/export.smk b/nextclade/rules/export.smk
@@ -4,19 +4,21 @@ export a reference tree and create the Nextclade dataset.
 
 REQUIRED INPUTS:
 
-    TODO: Confirm inputs for Nextclade v3
-    reference           = ../shared/reference.fasta
-    pathogen            = config/pathogen.json
-    genome_annotation   = config/genome_annotation.gff3
-    readme              = config/README.md
-    changelog           = config/CHANGELOG.md
-    metadata            = data/metadata.tsv
-    tree                = results/tree.nwk
-    branch_lengths      = results/branch_lengths.json
-    nt_muts             = results/nt_muts.json
-    aa_muts             = results/aa_muts.json
-    clades              = results/clades.json
-
+    augur export:
+        metadata            = data/metadata.tsv
+        tree                = results/tree.nwk
+        branch_lengths      = results/branch_lengths.json
+        nt_muts             = results/nt_muts.json
+        aa_muts             = results/aa_muts.json
+        clades              = results/clades.json
+
+    Nextclade dataset files:
+        reference           = ../shared/reference.fasta
+        pathogen            = config/pathogen.json
+        genome_annotation   = config/genome_annotation.gff3
+        readme              = config/README.md
+        changelog           = config/CHANGELOG.md
+        example_sequences   = config/sequence.fasta
 
 OUTPUTS: