Change the input files to only take one transcriptome assembly file instead of two

PR checklist

[x] Tag the issue(s) or milestones this PR fixes (e.g. Fixes #123, Resolves #456).
[x] Describe the changes you've made.
[x] Describe any tests you have conducted to confirm that your changes behave as expected.
[x] If you've added new software dependencies, make sure that those dependencies are included in the appropriate conda environments.
[x] If you've added new functionality, make sure that the documentation is updated accordingly.
[x] If you encountered bugs or features that you won't address, but should be addressed eventually, create new issues for them.

This PR addresses #42
It refactors the code, input files, and rewrites the relevant documentation to make only one transcriptome input file.
I ran the changes through the demo data and confirmed we got the same results.