Bactopia

Latest version: v1.3.0

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1.4.6

`Added`
- Option to rebuild conda envs to default location
- Updated fastq-dl for sra-toolkit forced interaction workaround

1.4.5

`Fixed`
- `--min_basepairs` and `--min_reads` not being honored

1.4.4

`Fixed`
- `annotate_genome` name clashes
- Updated `fastq-dl` version to support new ENA API endpoint

1.4.3

`Added`
- `--skip_ariba` option in `bactopia datasets`

`Fixed`
- `bactopia versions` and `bactopia citations` improper execution
- Convert spaces to tabs in citation doc
- Corrected CheckM name in program version info file
- CARD no longer default Ariba dataset download for `bactopia datasets`

1.4.2

`Added`
- added requirement checks of `--accessions` in `bactopia datasets`
- improved ENA spell check for species name

`Fixed`
- file of accessions not working with `bactopia datasets`
- Dockerfile and Singularity being missed by `update-version.sh`

1.4.1

`Added`
- Links to publication (woohoo!)
- Can pass a Prodigal training file to `bactopia datasets`

`Fixed`
- Typos in the Docs
- blast_primers now uses `blastn` and blast_genes uses `megablast`
- validExitStatus deprecation warning

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