Bactopia

`Added`
- `bactopia build` to build Conda environments
- Version info pulled from nextflow.config
- Set default values resource allocations
- Documentation on new changes
- Automatic building of Conda environments, if none exist
- `--nfdir` to determine where bactopia is being run from

`Fixed`
- Never ending typos
- `--datasets` now, not `--dataset` <-(Typo)
- path for outputting Nextflow reports
- Typo in antimicrobial_resistance.sh (task.cpus not cpus)
- `--species` is now consistent between `bactopia` and `bactopia datasets`
- Bug when checking if specific species dataset exists, but no species datasets exist
- Cleaned up version update script
- Cleaned up usage

`Removed`
- `--max_cpus` ability to limit total cores used, access to config is being deprecated in Nextflow
- `--max_cpus` since it is redudant to `--cpus` now

`Added`
- `--compress` to compress certain outputs, default uncompressed
- Species name check in `bactopia datasets`
- Use requests package instead of urllib3
- Added `bactopia search` to query ENA for list of Illumina accessions
- Documentation
- Feedback edits
- Output overview
- Additional program acknowledgements
- bibtex of citations
- missing parameters to usage
- info for `--genome_size` parameter
- `bactopia search` usage
- Workflow overview
- blastdbcmd compatible seqid to assembly fasta
- allows search for entries with sample name
- Mask low coverage regions in consensus (subs only) fasta
- Added --dry_run to build conda envs one at a time (prevent parallel issues)
- Added Singularity recipes
- Added SLURM config

`Fixed`
- Never ending typos
- `bactopia datasets` lowercase species names not found in MLST schemas
- `bactopia version` no longer calls nextflow
- SEQUENCE_TYPE channel groups FASTQ and assembly
- MINMER_QUERY channel groups FASTQ and signature
- Ariba MLST always running with `--noclean`
- Bugs related `--compress`
- Reduced size of per-base coverage outputs
- Removed `-parse_seqids` from makeblastdb command, caused blast queries to fail
- genomeCoverageBed failing on empty BAM files

`Removed`
- `--clean_cache` function

- fixed `bactopia-summary` not working with Bakta annotations
- added support for alternative extensions in `bactopia-atb-formatter` nickjhathaway 🎉

`Added`
- NCBI's amrfinder
- Dockerfile for main bactopia install
- Completed documentation!

`Fixed`
- insertion_sequences inputs are not now grouped into single channel
- Unintended FASTQ duplication via poor publishDir pattern

- added `bactopia-atb-formatter` to format All-the-Bacteria assemblies for Bactopia

- Fixed `bactopia-prepare` usage of `--prefix` not working