feat: make chopper default for longread qc

[dialvarezs]

• Makes chopper the default long read filtering tool instead of filtlong. Chopper does the same job with less overhead; filtlong and nanoq stay available via --longread_filtering_tool.

• Adds --longread_filtering_by_shortreads (default: false). Before this, filtlong always tried to join short and long reads to derive quality from k-mer matches, which could drop long reads that didn't overlap the short read set. Now that behavior is opt-in.

• test_hybrid pins --longread_filtering_tool filtlong explicitly since the default changed.

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
• If necessary, also make a PR on the nf-core/mag branch on the nf-core/test-datasets repository.
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• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).