* Updating README to fix argument, email, and formatting

* removing superfluous files

* Add link to CRISPRessoPro, move CRISPRessoPro section to end, and fix JSON formatting

* Remove link to CRISPRessoPro

* Replace Docker badge with link to tags

* Add bullet points to Guardrails section and improve formatting

* Fix typo and removed colons from guardrails

---------

Co-authored-by: Cole Lyman <cole@colelyman.com>

* Extract jinja_partials code

* Remove Plotly dependency from setup.py

* Fix replacing flash intermediate files with fastp intermediate files

This also moves where the files are added to `files_to_remove` up to
near where they are created.

* Update to run test branch with paired end Pooled test

* Add pooled-paired-sim test to integration tests

* Replace flash and trimmomatic with fastp and remove plotly from Github Actions environment

* Change test branch back to master