fix: modify cutadapt args for paired-end

[kelly-sovacool]

Changes

• Uses -m X:X and both -b -B for paired end reads
• The test now checks the command line arguments used for cutadapt to make sure they're passed correctly.

Issues

resolves #9

PR Checklist

(Strikethrough any points that are not applicable.)

• This comment contains a description of changes with justifications, with any relevant issues linked.
• Write unit tests for any new features, bug fixes, or other code changes.
• [ ] Update docs if there are any API changes.
• [ ] Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/