ID strain by accession

nextstrain · Sep 13, 2023 · fac7373 · fac7373
1 parent 81a072a
commit fac7373
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/Snakefile b/Snakefile
@@ -104,6 +104,7 @@ rule filter:
         augur filter \
             --sequences {input.sequences} \
             --metadata {input.metadata} \
+            --metadata-id-columns accession \
             --exclude {input.exclude} \
             --output {output.sequences} \
             --group-by {params.group_by} \
@@ -172,6 +173,7 @@ rule refine:
             --tree {input.tree} \
             --alignment {input.alignment} \
             --metadata {input.metadata} \
+            --metadata-id-columns accession \
             --output-tree {output.tree} \
             --output-node-data {output.node_data} \
             --timetree \
@@ -234,6 +236,7 @@ rule traits:
         augur traits \
             --tree {input.tree} \
             --metadata {input.metadata} \
+            --metadata-id-columns accession \
             --output {output.node_data} \
             --columns {params.columns} \
             --confidence \
@@ -276,6 +279,7 @@ rule export:
         augur export v2 \
             --tree {input.tree} \
             --metadata {input.metadata} \
+            --metadata-id-columns accession \
             --node-data {input.branch_lengths} {input.traits} {input.clades} {input.nt_muts} {input.aa_muts} \
             --auspice-config {input.auspice_config} \
             --include-root-sequence \