Remove checkpoints (#107)

* feat: add a 'profile/local' profile that does not run with a cluster

* feat: parse the snakemake `config` object into a type-hinted dataclass

* feat: add directory options for benchmarks and logs

* feat: create enter/exit dunder methods for `NCBI` class

* feat: download cdna fasta file for salmon

* refactor: use `with Path(...).open()` to open files for I/O

* feat: add `--log` cli option; write logs to file if provided

* feat: create environments for gffread and salmon

* feat: update fastq-screen to 0.16.0

* refactor: do not require httpx for rich for STAR environment

* refactor: remove `pyproject.toml` as it is not required

* feat: remove checkpoints from Snakefile for deterministic file processing; use type-hinted objects to parse data

Author: JoshLoecker