Bactopia

- added:
- `bactopia-pubmlst-setup` to setup PubMLST REST API connections
- `bactopia-pubmlst-build` to build PubMLST databases compatible with `mlst` Bactopia Tool

`Added`
- `summary` tool now gives reason for rank
- `summary` tools now splits `failed` into `exclude` and `qc-failure`
- Better documentation on how `--cpus` works in Nextflow
- Efficiency info when executed on standard profile
- split `blast_query` into `blast_genes`, `blast_primers` and `blast_proteins`
- `mapping_query` now creates multifasta of fastas at maps at once then splits per-base coverage into separate files
- `--nfconfig` users can provide their own Nextflow config file
- `fastani` users can provide their own reference now
- `bactopia versions` will print versions for tools used by Bactopia
- `bactopia citations` will print citations for tools and datasets used by Bactopia
- `bactopia search` can filter based on total bases, mean read length, and missing FASTQs
- blast queries results are only JSON format for easy parsing later
- added `--compliant` option for Prokka annotation

`Fixed`
- build-containers.sh not working with Bactopia Tools
- Bactopia Tools container tools missing environment.yml
- Typo in `fastani` usage
- Samples with multiple QC errors counted for each error
- Incorrect ISMapper version
- typo in `summary` SLURM profile
- `gtdb` Singularity container not mounting path to GTDB database
- `roary` missing `rename` in containers
- `blast_query` results overwriting one another
- `build-containers.sh` now creates a "latest" tag
- `bactopia tool roary` outputs results based on the given prefix
- renamed `--addgenes` to `--nogenes`
- updated ASA³P citation
- Typos in Bactopia Tools docs
- Link in README.md

- replace conda/mamba `--force` with simple `rm -rf`
- latest version of mamba removed `--force`

`Added`
- `--conda_help` to be used for conda build test
- `--skip_fastq_check` to skip check that input FASTQs meet minimum requirements
- Undocumented parameters to the usage

`Fixed`
- snippy not working with samtools 1.10
- NXF_HOME variable is exported to the conda env location
- speed of checking if conda environments are built

`Added`
- select-references selects latest assembly accession version (BioPython/Entrez)
- select-references skips assemblies that have been excluded from RefSeq
- test to for paired-end related errors (e.g. different read counts)
- `--min_genome_size` and `--max_genome_size` parameter for estimated genome sizes
- Check is also made after assembly
- `update-version.sh` improvements
- Better genome size estimates using Mash for high and low coverage sequences
- Script to update conda environments
- added `--conda_help` to be used for conda build test

`Fixed`
- `--random_tie_break` always true
- not using latest assembly accession for ncbi-genome-download
- usage of assemblies that have been excluded from RefSeq
- allowing PE reads with different read counts to be processed (hint... they fail pretty quickly)
- failure to stop analysis of sample with low read counts
- coverage reported as 'inf'
- references to cgmlst in the setup datasets
- non-explicit patterns in publishDir
- low coverage/read errors after QC were not put in root dir
- snippy not working with samtools 1.10

`Added`
- Size of "work" directory to the execution summary
- User controlled overwrites of existing output files
- Check for unknown parameters at runtime
- FASTQ downloads from SRA (via fastq-dl and fasterq-dump)
- Documentation updates
- Script for building containers

`Fixed`
- `bactopia` command now explicitly states which tag to use for Nextflow run
- Version info not updated in Dockerfile and Singularity
- Duplicated QC'd FASTQs
- nextflow: docker "Memory limited without swap" error

`Removed`
- cgmlst support in `bactopia datasets`
- setup.py left over from pre-conda config