Bactopia

- actually remove `--force` from `mamba|conda` commands

`Added`
- `bactopia build` checks if each environment is built before building
- Can specify `bactopia build` to build a specific environment
- Removed build numbers in Conda environment yamls
- Created separate Conda yamls for Linux and Mac
- NCBI assembly accessions will retrieve the most current version (e.g. .1, .2, .3, etc...)

`Fixed`
- `bactopia datasets` trailing whitespace in species names
- `bactopia datasets` random subsample missing specified species when `--limit` and `--include_genus` used
- GitLab CI OSX compatibility
- Adaptive resource allocations
- Datasets are checked for existence
- Variant calls against references with multiple chromosomes

`Added`
- `card` is back as a default Ariba dataset
- Added timestamps to `versions` files

`Fixed`
- `bactopia search` not creating `--outdir`
- `gtdb` tool not using prefix in outdir naming
- `pirate` tool using pangenome alignment instead of core
- Use of `scratch` causing logs to fail

`Added`
- Support for multiple accession
- `bactopia search` (SRA)
- Bactopia Tools: `fastani`, `mashtree`, `pirate`, `roary` (Assembly)

`Fixed`
- Undefined variable in `mapping_query.sh`
- ENA API endpoint for `bactopia search`
- Updated GTDB-TK to 1.3.0 to support latest downloads
- FastANI tool merge_results in no longer a separate step
- ANI is now one-to-many calculations
- `--reassemble` misapplied

`Added`
- Versions are logged for Bactopia
- STDOUT/STDERR logs are kept for each sample
- can be skipped using `--skip_logs`

`Fixed`
- Long sample names breaking Prokka annotation
- Syntax errors in Bactopia tools
- null values being tested as integers
- Ariba card and mlst downloads not working
- missing parameter in GTDB Bactopia tool

`Added`
- `--no_cache` to skip caching ncbi assembly info