Resolve "Move inference to start of pipeline"

Please fill in the appropriate checklist below (delete those which are not relevant). These are the most common things requested on pull requests.

PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated
• Replace dag.png with the most recent CI pipleine integrated_pe artifact
• README.md is updated

• Close issue
  Closes #47 (closed)

/cc @ghenry @venkat.malladi

Moves metadata (species, endness, spike, stranded) to the start of the pipeline and does not use any user entered metadata for any downstream processes