Bactopia

`Added`
- tweaks to the CI (via GitHub Actions)
- docker containers use quay.io now
- docker containers now use conda-pack
- `--nfconfig` will skip the conda environment build step
- input accessions are checked to be Assembly or Experiment accessions
- improved version increment script
- executor profiles can be configured by parameters

`Fixed`
- phyloflash and download_reference environment errors
- environment path in Bactopia Tools Dockerfile and Singularity recipes
- moved version from conda yaml to conda version file
- streamlined Docker recipes
- undefined `--ftp_only` message
- typo in singularity profile
- stderr logged to file is also printed to screen
- `qc_reads` memory used now determined by base config

`Added`
- `--prefix` option for `bactopia prepare`
- date is included in `bactopia summary` output

`Fixed`
- removed usage personal (rpetit3) conda channel
- aspera connect no longer supported
- shovill-se is now used from Bioconda
- updated conda environments (phyloflash broken)

`Fixed`
- quoted arguments being broken up (e.g. `--species "Staphylococcus aureus` -> `--species Staphylococcus`)
- `mashtree` tool failure to download with `--accessions`
- remove ncbi-genome-download header when using `--dry-run`
- undefined `name` variable in plasmid_blast
- custom work dir causing two `-w` parameters
- `bactopia search` results now contains all (illumina and non-illumina)

`Added`
- Changelog moved to docs
- recursive search for `bactopia prepare`
- allow multiple FASTQs per sample (FASTQs are merged)

`Fixed`
- unable to run `bactopia datasets` without parameters
- PLSDB blast results in invalid JSON format
- Error message for unaccepted `run_type`

`Fixed`
- `--skip_qc` causing "file not found"
- `qc_reads` not honoring FINAL_BP and FINAL_READS checks

`Fixed`
- `bactopia tools` not a valid project name
- `bactopia tools` `--cleanup_workdir` unrecognized variable