Add a --query option for when there is only one query

[charles-plessy]

Closes #112

This is inspired by nf-co.re/demultiplex, which also allows to bypass --input and provide single files directly.

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
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• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[piplus2]

I think the event with both --input and --query should be handled with a feedback to the user, or that the priority should go into the help.

[piplus2]

🚀