[WIP] Fix Nextflow file location errors with relative paths

[Copilot]

Thanks for assigning this issue to me. I'm starting to work on it and will keep this PR's description up to date as I form a plan and make progress.

Original prompt

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This section details on the original issue you should resolve

<issue_title>Nextflow relative paths</issue_title>
<issue_description>There's been a lot of errors with the file locations with hardcoded paths. several options beyond just using a relative path, such as using data roots or making another config file. Standard nextflow options should be used.</issue_description>

<agent_instructions>Please use the best option as if you were a professional software developer expert in Nextflow</agent_instructions>

Comments on the Issue (you are @copilot in this section)

• Fixes Nextflow relative paths #1

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