Resolve "process_qc"

Primarily QC processes (including multiqc)... Also includes A LOT of small changes (including minor refactoring to harmonize io and logging)...

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
• CHANGELOG.md is updated
• README.md is updated
• LICENSE.md is updated with new contributors

• Close issue
  Closes #10 (closed) Closes #51 (closed)

/cc @ghenry @venkat.malladi