fix: increase file latency wait

[kelly-sovacool]

Changes

Increase the latency wait to 300, and use realpaths where possible.

Issues

• resolves snakemake jobs failing due to missing output files which do exist #123
• oddly, this also appears to resolve ciri failing even with 3 retries #128 and resolve star1p slurm job failing even though rule succeeds #127

PR Checklist

(Strikethrough any points that are not applicable.)

• This comment contains a description of changes with justifications, with any relevant issues linked.
• [ ] 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/