Merge pull request #70 from nextstrain/nextclade-v3

Update nextclade workflow docs for v3
nextstrain · Oct 22, 2024 · 71feb33 · 71feb33
2 parents 22e8458 + 23d6072
commit 71feb33
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Showing 2 changed files with 16 additions and 14 deletions.
diff --git a/nextclade/build-configs/test-dataset/test_dataset.smk b/nextclade/build-configs/test-dataset/test_dataset.smk
@@ -12,7 +12,7 @@ rule test_dataset:
         dataset_dir="datasets/{build_name}",
     shell:
         """
-        nextclade2 run \
+        nextclade3 run \
             {input.sequences} \
             --input-dataset {params.dataset_dir} \
             --output-all {output.outdir}

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: