fix(cli): allow --output-annotation-gff and --output-annotation-tbl as sole args

[ivan-aksamentov]

Resolves: #1707

[Copilot]

Pull request overview

This PR fixes a bug where the CLI flags --output-annotation-gff, --output-annotation-tbl, and --output-tree-nwk could not be used as sole output arguments. The fix adds these flags to the validation logic that checks whether at least one output flag is provided, allowing them to be used independently without requiring other output flags.

• Adds three output flags to the validation array in nextclade_get_output_filenames()
• Updates the error message to list all valid output flags including the newly supported ones
• Updates test expectations to reflect the corrected error message

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

File	Description
packages/nextclade-cli/src/cli/nextclade_cli.rs	Adds output_tree_nwk, output_annotation_gff, and output_annotation_tbl to both the validation array and error message in the output validation logic
tests/functional/nextclade_run_args.t	Updates test expectations to match the corrected error message that now includes the three additional output flags

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[github-actions]

Preview: https://nextstrain--nextclade--pr-1708.previews.neherlab.click

(ci)