fix: use filter aligned output for samToFastq input

[kelly-sovacool]

Changes

previously it was just passing bwa mem to samtofastq instead of using the filtered output

Issues

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/