Merge pull request #1708 from nextstrain/fix/cli-output-tbl-gff

Author: ivan-aksamentov

packages/nextclade-cli/src/cli/nextclade_cli.rs

@@ -953,6 +953,9 @@ Example for bash shell:
     output_csv,
     output_tsv,
     output_tree,
+    output_tree_nwk,
+    output_annotation_gff,
+    output_annotation_tbl,
   ]
   .iter()
   .all(|o| o.is_none())
@@ -970,7 +973,10 @@ At least one of the following flags is required:
   --output-csv
   --output-tsv
   --output-tree
-  --output-translations"#
+  --output-tree-nwk
+  --output-translations
+  --output-annotation-gff
+  --output-annotation-tbl"#
     );
   }
 

tests/functional/nextclade_run_args.t

@@ -19,9 +19,10 @@ Nextclade run: no output args
           --output-csv
           --output-tsv
           --output-tree
+          --output-tree-nwk
           --output-translations
-          --output-insertions
-          --output-errors\x1b[0m (esc)
+          --output-annotation-gff
+          --output-annotation-tbl\x1b[0m (esc)
 
   Location:
      \x1b[35mpackages/nextclade-cli/src/cli/nextclade_cli.rs\x1b[0m:\x1b[35m710\x1b[0m (esc)