Bactopia

`Added`

- Updated `bactopia-assembler` to include updated Medaka models
- profile for `arcc_hawk`
- TB Profiler results are now merged with `collate` command
- sample name to plasmidfinder results
- support config files from nf-core/configs
- updated AMRFinder+ database for v3.12.8
- bump program versions in modules
- `abritamr`: 1.0.14 -> 1.0.17
- `bactopia-assembler`: 1.0.3 -> 1.0.4
- `bactopia-teton`: 1.0.1 -> 1.0.2
- `bactopia-variants`: 1.0.1 -> 1.0.2
- `bakta`: 1.8.2 -> 1.9.3
- `blast`: 2.14.1 -> 2.15.0
- `busco`: 5.5.0 -> 5.7.0
- `gubbins`: 3.3.0 -> 3.3.4
- `multiqc`: 1.15 -> 1.21
- `mashtree`: 1.4.5 -> 1.4.6
- `mykrobe`: 0.12.2 -> 0.13.0
- `ncbi-amrfinderplus`: 3.11.18 -> 3.12.8
- `panaroo`: 1.3.3 -> 1.4.2
- `rgi`: 6.0.2 -> 6.0.3
- `sistr`: 1.1.1 -> 1.1.2
- `stecfinder`: 1.1.0 -> 1.1.1
- `tbprofiler`: 5.0.0 -> 6.1.0

`Fixed`

- variable name in sketcher module
- `--para-off` not correctly implemented in PIRATE module
- extra space in RGI container image name
- sourmash version STDERR not parsed out
- FASTQC writing to /tmp dir on HPC when non-readable
- abricate and ariba not using output subdirectory
- nextflow tower typos iferres
- phispy not working with Bakta genbank files
- missed check of `--download_bakta` param in main workflow
- quast not working when estimated genome size is 0
- `abricate` now gets database subdirectories

`Enhancements to OSS`

- fix amrfinderplus pinning in abritamr [bioconda/bioconda-recipes46714](https://github.com/bioconda/bioconda-recipes/pull/46714)
- adjust python pinning in gubbins [bioconda/bioconda-recipes46713](https://github.com/bioconda/bioconda-recipes/pull/46713)
- fix issue with sistr container [bioconda/bioconda-recipes46712](https://github.com/bioconda/bioconda-recipes/pull/46712)
- update rgi pinning for pyrodigal [bioconda/bioconda-recipes46669](https://github.com/bioconda/bioconda-recipes/pull/46669)
- pin tabix version in snippy [bioconda/bioconda-recipes46458](https://github.com/bioconda/bioconda-recipes/pull/46458)

`Added`
- Bactopia Tools (`bactopia --wf <NAME>`)
- `abritamr` - A NATA accredited tool for AMR detection
- `blastn` - Search against nucleotide BLAST databases using nucleotide queries
- `blastp` - Search against protein BLAST databases using protein queries
- `blastx` - Search against protein BLAST databases using translated nucleotide queries
- `bracken` - Taxonomic classification and species abundance estimation of sequence reads
- `btyper3` - Taxonomic classification of Bacillus cereus group isolates
- `midas` - Estimate bacterial species abundances from FASTQ files
- `quast` - Assess the quality of assembled contigs
- `phispy` - Predict prophages in bacterial genomes
- `pneumocat` - Assign capsular type to Streptococcus pneumoniae from sequence reads
- `sra-human-scrubber` - Scrub human reads from FASTQ files
- `stecfinder` - Serotyping Shigella toxin producing Escherichia coli genomes
- `tblastn` - Search against translated nucleotide BLAST databases using protein queries
- `tblastx` - Search against translated nucleotide BLAST databases using translated nucleotide queries
- per-release databases for `amrfinderplus` and `mlst`
- new directory structure for outputs
- Renamed `--R1`, `--R2`, and `--SE` to `--r1`, `--r2`, and `--se`
- `--ont` now accepts a FASTQ file
- GitHub Action to build environments
- `fastp` is default read cleaner, can use previous methods with `--use_bbmap`
- ability to use a BED file to mask regions in `snippy-core`
- `--save_sketches` to save Mash sketches created during `mashtree` run5
- Porechop is now optional (`--use_porechop`)
- unified `publishDir` across modules
- download datasets using `storeDir`
- `BACTOPIA:DATASETS`
- `ariba`
- `sra-human-scrubber`
- bump program versions in modules
- `bakta`: 1.6.0 -> 1.8.2
- `blast`: 2.11.0 -> 2.14.1
- `busco`: 5.4.3 -> 5.5.0
- `csktk`: 0.25.0 -> 0.27.2
- `eggnog-mapper`: 2.1.9 -> 2.1.12
- `genotyphi`: 1.9.1 -> 2.0
- `gtdbtk`: 2.1.1 -> 2.3.2
- `gubbins`: 3.2.1 -> 3.3
- `iqtree`: 2.2.0.3 -> 2.2.2.7
- `fastani`: 1.33 -> 1.34
- `mashtree`: 1.2.0 -> 1.4.5
- `mob_suite`: 3.1.0 -> 3.1.7
- `multiqc`: 1.11 -> 1.15
- `mykrobe`: 0.12.0 -> 0.12.2
- `ncbi-amrfinderplus`: 3.10.45 -> 3.11.18
- `ncbi-genome-download`: 0.3.1 -> 0.3.3
- `panaroo`: 1.3.0 -> 1.3.3
- `pasty`: 1.0.0 -> 1.0.3
- `phyloflash`: 3.4 -> 3.4.2
- `rgi`: 6.0.1 -> 6.0.2
- `shigatyper`: 2.0.3 -> 2.0.5
- `shigeifinder`: 1.3.2 -> 1.3.5
- `tbprofiler`: 4.4.0 -> 5.0.0

`Fixed`
- All modules correctly initiate `params.options`
- OpenJDK java cpuset warning message (idolawoye)
- Broken badges in README.md
- Pinned GSL to v2.6
- symlink in amrfinder+ update (`bactopia datasets`)
- hardcoded `--plus` in `amrfinderplus_run`
- tests for new directory structure
- `--nanohq` not being properly passed to `dragonflye`

`Removed`
- Bactopia Steps
- `ANNOTATE_GENOME` - now handled by `prokka` or `bakta`
- `ANTIMICROBIAL_RESISTANCE` - now handled by `amrfinderplus`
- `CALL_VARIANTS` - now handled by `snippy`
- `SEQUENCE_TYPE` - now handled by `mlst`
- `bactopia datasets` is now incorporated into `bactopia`
- Conda/Containers for all bactopia-main steps
- custom process labels, for generic `nf-core` process labels

`Enhancements to OSS`
- add module for midas [nf-core/modules2696](https://github.com/nf-core/modules/pull/2696)
- add modules for sra-human-scrubber [nf-core/modules2694](https://github.com/nf-core/modules/pull/2694)
- add module for stecfinder [nf-core/modules2702](https://github.com/nf-core/modules/pull/2702)
- update midas pinnings to match docs [bioconda/bioconda-recipes38566](https://github.com/bioconda/bioconda-recipes/pull/38566)
- add missing scripts to MLST [bioconda/bioconda-recipes38826](https://github.com/bioconda/bioconda-recipes/pull/38826)
- fix GTDB-Tk container [bioconda/bioconda-recipes40333](https://github.com/bioconda/bioconda-recipes/pull/40333)
- patch ncbi-genome-download [bioconda-recipes41640](https://github.com/bioconda/bioconda-recipes/pull/41640)
- add module for pneumocat [nf-core/modules3592](https://github.com/nf-core/modules/pull/3592)
- add module for abritamr/run [nf-core/modules3725](https://github.com/nf-core/modules/pull/3725)
- fix hostrange() missing 1 required positional argument: 'database_directory' [phac-nml/mob-suite149](https://github.com/phac-nml/mob-suite/pull/149)
- add module for btyper3 [nf-core/modules3817](https://github.com/nf-core/modules/pull/3817)

`Added`
- `--dragonflye_opts` to pass additional params to dragonflye
- `--use_fastp` to use fastp for QCing reads
- `bactopia datasets` no longer depends on `ariba`
- `--skip_spell_check` in `bactopia datasets`
- updated organisms available from PubMLST
- custom profile for `wsvl`
- updated citations
- use `mambaforge` for docker builds
- Support tarball inputs for large databases
- Bactopia Tools (`bactopia --wf <NAME>`)
- `pasty` - in silico serogrouping of _Pseudomonas aeruginosa_ isolates
- `pbptyper` - In silico Penicillin Binding Protein (PBP) typer for _Streptococcus pneumoniae_ assemblies
- `shigeifinder` - Serotyping Shigella and EIEC assemblies
- bump program versions in modules
- `bakta` -> 1.5.1
- `bbmap` -> 39.01
- `checkm-genome` -> 1.2.2
- `csvtk` -> 0.25.0
- `dragonflye` -> 1.0.13
- `eggnog-mapper` -> 2.1.9
- `fastani` -> 1.33
- `fastq-scan` -> 1.0.1
- `gamma` -> 2.2
- `gtdbtk` -> 2.1.1
- `iqtree` -> 2.2.0.3
- `kleborate` -> 2.2.0
- `mlst` -> 2.23.0
- `mob_suite` -> 3.1.0
- `mykrobe` -> 0.12.0
- `nanoplot` -> 1.40.2
- `ncbi-amrfinderplus`-> 3.10.45
- `panaroo` -> 1.3.0
- `pirate` -> 1.0.5
- `rasusa` -> 0.7.0
- `rgi` -> 6.0.1
- `shigatyper` -> 2.0.3
- `snpeff` -> 5.1
- `sourmash` -> 4.5.0
- `sra-tools` -> 3.0.0
- `tb-profiler` -> 4.4.0

`Fixed`
- respect short polish hybrid assembly requests
- missing variable in `bakta_download` module
- restructure to match `nf-core/modules`
- compatibility with Nextflow >=22.10
- separate versions for Linux and OSX in `assemble_genomes`
- `bactopia datasets` error messages switched to warnings

`Enhancements to OSS`
- bump Bakta to 1.5.0 [nf-core/modules2000](https://github.com/nf-core/modules/pull/2000)
- add recipe for pasty [bioconda/bioconda-recipes35930](https://github.com/bioconda/bioconda-recipes/pull/35930)
- add recipe for pbptyper [bioconda/bioconda-recipes36222](https://github.com/bioconda/bioconda-recipes/pull/36222)
- add module for pasty [nf-core/modules2003](https://github.com/nf-core/modules/pull/2003)
- add module for pbptyper [nf-core/modules2005](https://github.com/nf-core/modules/pull/2005)
- add module for shigeifinder [nf-core/modules2523](https://github.com/nf-core/modules/pull/2523)

`Added`
- Add Panaroo to the `pangenome` Bactopia Tools
- Add `genotyphi` and `seroba` to Merlin
- bump `fastq-dl` to v1.1.1
- Bactopia Tools (`bactopia --wf <NAME>`)
- `busco` - Assembly completeness based on evolutionarily informed expectations
- `genotyphi` - Salmonella Typhi genotyping with Mykrobe outputs
- `gubbins` - Rapid phylogenetic analysis of recombinant bacterial sequences
- `mcroni` - Sequence variation in mobilized colistin resistance (mcr-1) genes
- `mykrobe` - Antimicrobial resistance detection for specific species
- `panaroo` - Pipeline for pangenome investigations
- `plasmidfinder` - Plasmid identification from assemblies
- `seroba` - Serotyping of Streptococcus pneumoniae from sequence reads
- `snippy` - Rapid variant calling from Illumina sequence reads with optional core-SNP phylogeny

`Fixed`
- improve GTDB db handling
- Properly capture assemblies with 0
- user provided adapters and phix fastas
- `--available_datasets` in the `bactopia datasets`
- name collisions in the Ariba Bactopia Tool
- bare double-quotes in Ariba reports
- updated tests for new version

`Enhancements to OSS`
- Add database to Seroba recipe [bioconda/bioconda-recipes35378](https://github.com/bioconda/bioconda-recipes/pull/35378)
- Update ariba dependencies [bioconda/bioconda-recipes35383](https://github.com/bioconda/bioconda-recipes/pull/35383)
- patch pymummer recipe [bioconda/bioconda-recipes35379](https://github.com/bioconda/bioconda-recipes/pull/35379)
- Update PlasmidFinder for better container support [bioconda/bioconda-recipes35314](https://github.com/bioconda/bioconda-recipes/pull/35314)
- add module for ariba [nf-core/modules1731](https://github.com/nf-core/modules/pull/1731)
- add module for mcroni [nf-core/modules1750](https://github.com/nf-core/modules/pull/1750)
- add module for Mykrobe and GenoTyphi [nf-core/modules1731](https://github.com/nf-core/modules/pull/1818)
- add module for plasmidfinder [nf-core/modules1773](https://github.com/nf-core/modules/pull/1773)
- add module for Seroba [nf-core/modules1816](https://github.com/nf-core/modules/pull/1816)
- add module for snippy/core [nf-core/modules1855](https://github.com/nf-core/modules/pull/1855)
- let tempfile determine temp dir location [sanger-pathogens/seroba68](https://github.com/sanger-pathogens/seroba/pull/68)
- allow the user to specify temp dir or use the system default [sanger-pathogens/pymummer36](https://github.com/sanger-pathogens/pymummer/pull/36)

`Added`
- `--use_bakta` to replace Prokka with Bakta in main workflow
- Split Bakta into two processes `download` and `run`
- added `shigatyper` to Merlin
- custom profile for `arcc`
- `bactopia prepare` error message when nothing found, and `--examples` for example use cases
- renamed `--fastqs` to `--samples` to better reflect its usage (fastqs and assemblies)
- add `--check_samples` to validate user generated FOFNs
- `--short_polish` for short read polishing for long-read assemblies
- Moved Ariba to Bactopia Tools
- bump versions in Bactopia envs
- bump Bactopia Tool versions
- `amrfinder+` version to 3.10.30
- `gtdb` version to 2.1.0
- `mlst` version to 2.22.0
- Bactopia Tools (`bactopia --wf <NAME>`)
- `ariba` - Gene identification by local assemblies
- `gamma` - Identification, classification, and annotation of translated gene matches
- `shigatyper`: Shigella serotype from Illumina or Oxford Nanopore reads

`Fixed`
- nickjhathaway Fixed assembly_level in `bactopia datasets` and auto `call_variants`
- `bactopia search` now supports ONT reads
- `vcf-annotator` unable to write to `/dev/stdout`
- typo in `bactopia download` when using singularity
- `bactopia download` will not rebuild envs its already built in a run
- `--include_genus` with `bactopia datasets` now works with multiple samples
- Parameters to copy optional species-specific files in `bactopia datasets`
- Don't use `AUTO` for IQ-TREE cpus
- `gtdb` download working again
- empty FASTQs after adapter and phix removal
- low read count error for ONT samples
- Removed `sequence_type` environment

`Added`
- logo and new metro style workflow
- added `test` profile for easy testing
- `mashdist` now outputs a merged TSV
- print missing required parameters in Bactopia Tools
- bump bakta to v1.4.0

`Fixed`
- typo in `bakta` subworkflow
- `ismapper` not available in `bactopia-tools.nf`
- `kraken2` not available in `bactopia-tools.nf`
- Traits file being required for `pangenome`
- `mashtree` module not collecting all FASTA
- tests for ISMapper