v3.0.1

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-v3-announcement.mp4

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

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

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

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

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

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

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

v2.0.0

v2.0.0 bactopia/bactopia "Red Hawk" - 2021/12/05

With Bactopia v2 comes a lot of changes! I would like to extend a huge thanks to Davi Marcon and Abhinav Sharma for their work initially converting Bactopia to DSL2. Your efforts were the momentum I needed to get the ball rolling on Bactopia v2. Thank you very much for taking your time to make such a siginificant contribution!

Added

• support for Nanopore reads
• staphopia as a named pipeline (alias for bactopia --wf staphopia) for S. aureus genomes
• bactopia/bactopia-tests repo with test data
• walkthrough for testing
• bactopia-datasets/staphylococcus_aureus repo with curatated S. aureus datasets
• per-module testing via pytest (100+ tests and 7000+ outputs tested)
• per-module meta.yml and params.json for auto-building docs site
• framefork for adding new Bactopia Tools
• 19 total Bactopia Tools (bactopia --wf <NAME>)
  • Subworkflows (3)
    • eggnog: Functional annotation of proteins using orthologous groups and phylogenies
    • pangenome: Pangenome analysis with optional core-genome phylogeny
    • staphtyper: Determine the agr, spa and SCCmec types for Staphylococcus aureus genomes
  • Modules (16):
    • agrvate: Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.
    • bakta: Rapid annotation of bacterial genomes and plasmids
    • ectyper: In-silico prediction of Escherichia coli serotype
    • emmtyper: emm-typing of Streptococcus pyogenes assemblies
    • fastani: fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)
    • hicap: Identify cap locus serotype and structure in your Haemophilus influenzae assemblies
    • ismapper: Identify insertion sites positions in bacterial genomes
    • kleborate: Screening Klebsiella genome assemblies for MLST, sub-species, and other related genes of interest
    • lissero: Serogroup typing prediction for Listeria monocytogenes
    • mashtree: Quickly create a tree using Mash distances
    • meningotype: Serotyping of Neisseria meningitidis
    • ngmaster: Multi-antigen sequence typing for Neisseria gonorrhoeae
    • seqsero2: Salmonella serotype prediction from reads or assemblies
    • spatyper: Computational method for finding spa types in Staphylococcus aureus
    • staphopiasccmec: Primer based SCCmec typing of Staphylococcus aureus genomes
    • tbprofiler: Detect resistance and lineages of Mycobacterium tuberculosis genomes
• Use mamba instead of conda for env building
• Reduced total Conda envs/Docker containers down to 7 (previously 12 not including bactopia tools)
• default to compressed outputs (--skip_compression to output uncompressed outputs)
• Tutorial outputs made available
• update github actions

Fixed

• Cache issue causing -resume to fail
• amrfinder+ database not compatible error
• incorrectly parsed system memory

Adapted from nf-core

• nf-core pytest setup
• nf-core/modules for bactopia tools
  • Bactopia v2 release contributed 20+ modules to nf-core/modules
• nf-core/tools arg parser
  • adapted to import params and usage based on config file

Process Consolidation

• makeblastdb -> assemble_genome
• call_variants, download_reference -> call_variants
• fastq_status, estiamte_genome_size -> gather_samples
• count_31mers -> minmer_sketch

Removed

• bactopia tools -> Handled by Nextflow now (bactopia --wf <NAME>)
• bactopia versions -> Program versions are output ever run now.

v1.7.1

v1.7.1 bactopia/bactopia "Shellbuster" - 2021/06/04

Added

• bumped GTDB to v1.5.0
• added soft ulimit for staph-typer

Fixed

• Matched PIRATE's parameter syntax for the tools
• staph-typer now uses GetBaseName

'Removed'

• PLSDB references in bactopia datasets