v3.2.0 bactopia/bactopia "Black Bulls" 2025/03/21

"Black Bulls" is related to the best magic squad in Black Clover my kids currently watching

Added

• Bactopia Tools (bactopia --wf <NAME>)
  • checkm2 - Rapid assessment of genome bin quality using machine learning @maxlcummins
  • sylph - taxonomic profiling and genome querying for meta-genomic samples
• teton now outputs a bactopia sample sheet with species and genome size filled out
  • sizemeup uses the bracken output to determine genome size
• more metrics and helper text at end of runs
• snippy use a local directory for --tmpdir
• bactopia atb-downloader to download ATB assemblies by BioSample, TaxID, or species
• pangenome add SNP dists for both masked and unmasked alignments
• within task clean up to help reduce work directory size
  • gtdb: add --gtdb_keep_msa to keep GTDB MSA files, otherwise remove
  • kraken2: replace --remove_filtered_reads with --keep_filtered_reads to keep classified and unclassified reads
  • ncbigenomedownload: add --keep_genomes to publish downloaded genomes, default leave in work directory
    • this also affects Prokka annotations in the pangenome workflow
  • snippy: add --snippy_remove_bam to remove BAM files after variant calling
• support for custom databases in emmtyper @maxlcummins
• bump program versions in modules
  • amrfinderplus: 3.12.8 -> 4.0.19
  • bactopia-teton: 1.0.2 -> 1.1.1
  • bakta: 1.9.4 -> 1.11.0
  • busco: 5.7.1 -> 5.8.2
  • csvtk: 0.27.2 -> 0.31.0
  • gubbins: 3.3.5 -> 3.4
  • iqtree: 2.2.2.7 -> 2.3.6
  • kleborate: 3.0.9 -> 3.1.3
  • multiqc: 1.24.1 -> 1.27.1
  • panaroo: 1.5.0 -> 1.5.1
  • quast: 5.2.0 -> 5.3.0
  • sister: 1.1.2 -> 1.1.3
  • sylph: 0.6.1 -> 0.8.0
  • tbprofiler: 6.3.0 -> 6.6.2

Fixed

• debugging print in functions.nf
• fixed params.max_retry in local profiles
• nextflow.config accessing param vals before they are set
• removed lingering task.ext which were not used
• replace --singularity_cache_dir with --singularity_cache to match bactopia download
• gamma not checking for --gamma_db at runtime
• tests using single protein (typo in file name config)
• pangenome mislabeling pangenome tool used (was using the correct tool)
• downloaded genomes added to --bactopia directory for pangenome
• useless use of options.btype ?: in modules (it didn't actually do anything because options.btype was always empty)
• version capture in dragonflye and mlst
• mismatch in defensefinder conda and container versions
• kraken-bracken-summary.py failing with 0 unclassified reads @maxlcummins

v3.1.0 bactopia/bactopia "Dance Powder" 2024/09/22

"Dance Powder" is related to the Alabasta arc in One Piece which my kids currently on

Added

• Named Workflows
  • clean-yer-reads - Use Bactopia's read QC steps to Clean-Yer-Reads
    • Use clean-yer-reads, cyr or bactopia --wf cleanyerreads
  • teton - Host removal and taxon classification with estimated abundances
    • Use teton or bactopia --wf teton
• Bactopia Tools (bactopia --wf <NAME>)
  • clermontyping - Clermont's Escherichia phylogrouping
  • defensefinder - Systematic search of all known anti-phage systems
  • sccmec - SCCmec typing of Staphylococcus aureus genomes
  • scrubber - Remove human reads from FASTQ files
    • screen human reads with kraken2 (against human pangenome) or sra-human-scrubber
  • shigapass - Predict Shigella serotypes and differentiate Shigella, EIEC and non-Shigella/EIEC
• full support of config files from nf-core/configs
  • no longer prints efficiency for standard, docker, and singularity profiles
  • now required non-integer values for --max_time (e.g. 4.h) and --max_memory (e.g. 8.GB)
  • always import base.config
• amrfinderplus by combining results from genes, proteins and gff (coordinates)
• --amrfinder_db and --mlst_db to specify custom databases
• mlst and amrfinder databases can now be either a tarball or directory
• pangenome tool now uses panaroo as the default pangenome tool
• file with reference name and samples included for snippy run
• snippy can now use --accession to download a genbank file from NCBI
• replaced staphopiasccmec with sccmec in staphtyper
• bump program versions in modules
  • abritamr: 1.0.17 -> 1.0.19
  • bakta: 1.9.3 -> 1.9.4
  • blast: 2.15.0 -> 2.16.0
  • busco: 5.7.0 -> 5.7.1
  • checkm: 1.2.2 -> 1.2.3
  • defensefinder: 1.2.2 -> 1.3.0
  • gtdbtk: 2.3.2 -> 2.4.0
  • hicap: 1.0.3 -> 1.0.4 (@MartinVad)
  • kleborate: 2.3.2 -> 3.0.9
  • mobsuite: 3.1.8 -> 3.1.9
  • panaroo: 1.4.2 -> 1.5.0
  • pasty: 1.0.3 -> 2.2.1
  • pbptyper: 1.0.4 -> 2.0.0
  • seqsero2: 1.2.1 -> 1.3.1
  • stecfinder: 1.1.1 -> 1.21.2
  • tbprofiler: 6.1.0 -> 6.3.0

Fixed

• missing schema for clean-yer-reads and teton
• pinning of bioperl in prokka module with strict channel priority
• use --infile-list with csvtk concat to support 10k+ inputs
• pangenome when Bakta GFF (*.gff3) files are provided
• missing file export in gubbins
• writing to non-default values for --bactopia
• --include file on cloud storage (@rwilliams)
• import of ONT reads over illumina reads in certain bactopia tools (e.g. snippy) (Thanks D2)
• bactopia/datasets envs not being build by bactopia download
• snippy puts files in subdirectory based on reference name
• removed pneumocat from Merlin as it doesn't gracefully fail on negative results
• all the tests
• typo in bactopia-tools.nf (thank you! @pvanheus)

Enhancements to OSS

• pinn macsyfinder version in defense-finder bioconda/bioconda-recipes#46824
• add recipe for camlhmp bioconda/bioconda-recipes#47453
• add recipe for sccmec bioconda/bioconda-recipes#47600
• update recipe for genotyphi bioconda/bioconda-recipes#47664
• disable phone home snpeff bioconda/bioconda-recipes#48007
• clermontyping use share folder bioconda/bioconda-recipes#49372
• add recipe for scrubby bioconda/bioconda-recipes#49373
• rebuild pasty bioconda/bioconda-recipes#50068

v3.0.1 bactopia/bactopia "That's My Girl" - 2024/03/25

"That's My Girl" is a phrase my youngest says quite often when playing with her friends

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-recipes#46714
• adjust python pinning in gubbins bioconda/bioconda-recipes#46713
• fix issue with sistr container bioconda/bioconda-recipes#46712
• update rgi pinning for pyrodigal bioconda/bioconda-recipes#46669
• pin tabix version in snippy bioconda/bioconda-recipes#46458

v3.0.0 bactopia/bactopia "Black Cat and Brown Dog" - 2023/09/11

"Black Cat and Brown Dog" are in memory of Stinky ("Black Cat") and Twotee ("Brown Dog")

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/modules#2696
• add modules for sra-human-scrubber nf-core/modules#2694
• add module for stecfinder nf-core/modules#2702
• update midas pinnings to match docs bioconda/bioconda-recipes#38566
• add missing scripts to MLST bioconda/bioconda-recipes#38826
• fix GTDB-Tk container bioconda/bioconda-recipes#40333
• patch ncbi-genome-download bioconda-recipes#41640
• add module for pneumocat nf-core/modules#3592
• add module for abritamr/run nf-core/modules#3725
• fix hostrange() missing 1 required positional argument: 'database_directory' phac-nml/mob-suite#149
• add module for btyper3 nf-core/modules#3817

v2.2.0 bactopia/bactopia "Tornado Tempo" - 2022/11/28

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/modules#2000
• add recipe for pasty bioconda/bioconda-recipes#35930
• add recipe for pbptyper bioconda/bioconda-recipes#36222
• add module for pasty nf-core/modules#2003
• add module for pbptyper nf-core/modules#2005
• add module for shigeifinder nf-core/modules#2523

v2.1.1 bactopia/bactopia "Dragon Twister" - 2022/07/09

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-recipes#35378
• Update ariba dependencies bioconda/bioconda-recipes#35383
• patch pymummer recipe bioconda/bioconda-recipes#35379
• Update PlasmidFinder for better container support bioconda/bioconda-recipes#35314
• add module for ariba nf-core/modules#1731
• add module for mcroni nf-core/modules#1750
• add module for Mykrobe and GenoTyphi nf-core/modules#1731
• add module for plasmidfinder nf-core/modules#1773
• add module for Seroba nf-core/modules#1731
• add module for snippy/core nf-core/modules#1855
• let tempfile determine temp dir location sanger-pathogens/seroba#68
• allow the user to specify temp dir or use the system default sanger-pathogens/pymummer#36

v2.1.0 bactopia/bactopia "Silver Mist" - 2022/06/08

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

v2.0.3 bactopia/bactopia "King Cobra" - 2022/03/23

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

Full Changelog: v2.0.2...v2.0.3

v2.0.2 bactopia/bactopia "Black Mamba" - 2022/02/22

Added

• bactopia download which merges the bactopia build and bactopia pull commands
• modules can now use prebuilt envs
• --available_species to print the species in a bactopia dataset
• --bbduk_opts to fine tune bbduk
• set quay as default docker registry
• Let Nextflow handle stdout and stderr
• added hpsuissero, legsta, sistr, ssuissero to Merlin
• Bactopia Tools (bactopia --wf <NAME>)
  • amrfinderplus: Identify antimicrobial resistance in genes or proteins
  • abricate: Mass screening of contigs for antimicrobial and virulence genes
  • checkm: Assess the assembly quality of your samples
  • hpsuissero: Serotype prediction of Haemophilus parasuis assemblies
  • kraken2: Taxonomic classification of sequence reads
  • legsta: Typing of Legionella pneumophila assemblies
  • mlst: Scan contig files against PubMLST typing schemes
  • mobsuite: Reconstruct and annotate plasmids in bacterial assemblies
  • rgi: Predict antibiotic resistance from assemblies
  • sistr: Serovar prediction of Salmonella assemblies
  • ssuissero: Serotype prediction of Streptococcus suis assemblies

Fixed

• toInteger on null genome size
• Index out of bounds in mlst-blast.py (caused by non allele columns)
• FOFN will fail if sample name is null
• improve available workflow logic
• PIRATE not exporting gene_presence_absence.csv correctly
• channel imports for scoary workflow
• argument type mismatch when using --use_roary
• missing channel when agrvate not ran as staphtyper
• float required options to the top when missing
• broken tests due to changes
• bactopia datasets including hidden directories
• Bioperl pinnings for prokka and pirate

v2.0.1 bactopia/bactopia "Red Roc" - 2022/01/06

Added

• Merlin for auto selection of species-specific tools based
• --ask_merlin to execute the Merlin subworkflow in Bactopia
• Schema compatible with NF-Tower
• --skip_qc_plots to skip FastQC and Nanoplot
• Disable CheckM by default, must use --run_checkm
• --cluster_opts for passing additional options to SLURM
• inclusion of local files (assembly, gff) in some subworkflows
• workflow for dev conda builds
• all subworkflows can be imported on other workflows
• Bactopia Tools (bactopia --wf <NAME>)
  • gtdb: Identify marker genes and assign taxonomic classifications
  • mashdist: Calculate Mash distances between sequences
  • merlin: MinmER assisted species-specific bactopia tool seLectIoN

Fixed

• Resource over allocation for java related programs (-Xmx)
• ordering of skipped steps when --datasets not used
• logic in container selection for nf-core modules
• channel manipulation in ncbigenomedownload
• missing logic for fastani
• version captures in subworkflows
• spell check for species with [ or ] in their names
• version outputs for Staphtyper subworkflow
• use process names in version.yml
• CSVTK_CONCAT empty channels
• options.suffix now used as prefix in modules