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Changelog

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

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

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

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

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

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

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

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 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

v1.7.0 bactopia/bactopia "Chocobo Wand" - 2021/04/27

Added

  • Bactopia Tool staph_typer for agr, spa, and sccmec typing
  • --min_coverage parameter to filter based on min coverage

'Removed'

  • plasmid_blast no longer apart of main workflow

v1.6.5 bactopia/bactopia "Z's Trident" - 2021/03/30

Added

  • version pins to process envs

Fixed

  • syntax for sourmash 4.0

v1.6.4 bactopia/bactopia "Trident +1" - 2021/03/26

Added

  • added Python3.6+ to all environments

v1.6.3 bactopia/bactopia "Trident" - 2021/03/25

Added

  • extra fields to mlst-blast.py outputs
  • added Python3 to qc_reads environment

Fixed

  • rstrip on empty extra fields in mlst profile
  • different BLAST+ software versions mismatch
  • tbb pinnings
  • --help and --version for bactopia tools

v1.6.2 bactopia/bactopia "Fuscina" - 2021/03/19

Added

  • inputs are checked to be gzipped (this does not include FOFN)
  • --skip_amr to skip AMRFinder+ analysis
  • new bactopia tool for hicap
  • unicycler can be used for Illumina reads only (--assembler unicycler)

Fixed

  • AMRFinder+ software and database version mismatch
  • check-fastqs.py syntax errors with prints
  • ismapper tool processing of include/exclude files

v1.6.1 bactopia/bactopia "Obelisk" - 2021/02/22

Fixed

  • sample names with "." in them breaking auto variant calling
  • contig naming incompatible with GenBank

v1.6.0 bactopia/bactopia "Harpoon" - 2021/01/22

Added

  • bactopia pull to pre-build Singularity images
  • --singularity_cache parameter to set location of image downloads
  • --registry to choose Docker registry to use (DockerHub, GitHub, Quay)
  • --max_downloads sets maximum number of downloads (FASTQ/assembly) allowed at once
  • --min_time sets the minimum amount of time a job should be given
  • bactopia search now uses POST requests, and groups accessions into single query
  • strip HTML from FASTA headers used in BLAST
  • Dockerfiles now have conda.md5 label to determine if rebuild is necessary
    • MD5 is updated in Dockerfile when env is updated
  • AMRFinder+ database is now provided by bactopia datasets
  • Parameterized profile (slurm, awsbatch, etc...) variables
  • bactopia build
    • will retry in case of HTTP connection issues
    • --include_tool will build Bactopia Tool environments
  • GitHub Actions
    • build Docker containers on new release (or manual trigger)
    • test that the Conda environment yamls are still valid
    • test bactopia with conda on Linux and OSX
    • test bactopia on Linux with Docker and Singularity

Fixed

  • redundant environment version files
  • failed FASTQ/Assembly downloads no longer stop whole run
  • --max_retry is honored now
  • antimicrobial_resistance process honors amrdir variable
  • change directory antimicrobial_resistance to antimicrobial-resistance
  • rename check_staging.py to check-staging.py for consistency
  • Bactopia not producing valid exit code on failure

Removed

  • --containerPath variable is replaced by --singularity_cache
  • Native Singularity recipes, will now convert Docker to Singularity
  • docs are now on bactopia.github.io repo

v1.5.6 bactopia/bactopia "Metal Slime Earring" - 2021/01/13

Added

  • tweaks to the CI (via GitHub Actions)
  • docker containers use quay.io now
  • docker containers now use conda-pack
  • --nfconfig will skip the conda environment build step
  • input accessions are checked to be Assembly or Experiment accessions
  • improved version increment script
  • executor profiles can be configured by parameters

Fixed

  • phyloflash and download_reference environment errors
  • environment path in Bactopia Tools Dockerfile and Singularity recipes
  • moved version from conda yaml to conda version file
  • streamlined Docker recipes
  • undefined --ftp_only message
  • typo in singularity profile
  • stderr logged to file is also printed to screen
  • qc_reads memory used now determined by base config

v1.5.5 bactopia/bactopia "Avenger's Earring" - 2021/01/04

Added

  • --prefix option for bactopia prepare
  • date is included in bactopia summary output

Fixed

  • removed usage personal (rpetit3) conda channel
    • aspera connect no longer supported
    • shovill-se is now used from Bioconda
  • updated conda environments (phyloflash broken)

v1.5.4 bactopia/bactopia "Nemesis Earring" - 2020/12/17

Fixed

  • quoted arguments being broken up (e.g. --species "Staphylococcus aureus -> --species Staphylococcus)
  • mashtree tool failure to download with --accessions
  • remove ncbi-genome-download header when using --dry-run
  • undefined name variable in plasmid_blast
  • custom work dir causing two -w parameters
  • bactopia search results now contains all (illumina and non-illumina)

v1.5.3 bactopia/bactopia "Morion Earring" - 2020/12/04

Added

  • Changelog moved to docs
  • recursive search for bactopia prepare
  • allow multiple FASTQs per sample (FASTQs are merged)

Fixed

  • unable to run bactopia datasets without parameters
  • PLSDB blast results in invalid JSON format
  • Error message for unaccepted run_type

v1.5.2 bactopia/bactopia "Physical Earring" - 2020/11/18

Fixed

  • --skip_qc causing "file not found"
  • qc_reads not honoring FINAL_BP and FINAL_READS checks

v1.5.1 bactopia/bactopia "Astral Earring" - 2020/11/17

Fixed

  • bactopia tools not a valid project name
  • bactopia tools --cleanup_workdir unrecognized variable

v1.5.0 bactopia/bactopia "Cassie Earring" - 2020/11/12

Added

  • Conda environments will check if in sync with latest version now
  • md5sums of all conda envs
  • Verify species-specific datasets exist
  • separate work dir for bactopia and bactopia tools
  • --cleanup_workdir to delete work directory after successful run
  • default values for bactopia datasets summary.json
  • Fallback to NCBI Assembly when eUtils is down
  • Additional pre-process QC checks
  • OSX/Linux conda envs for Bactopia Tools
  • Documentation edits and updates
  • Bactopia and Nextflow versions are now output for logging purposes
  • option to skip QC step (--skip_qc)
  • bactopia datasets can now specify assembly level
  • bactopia tools now use reusable conda envs
  • bactopia tools for Roary and PIRATE can now include local assemblies

Fixed

  • Warn user if no completed genomes are available
  • use of --genera for ncbi-genome-download
  • improved genome_size handling
  • explicit file passing for AWS Batch
  • Memory estimates now floored
  • PLSDB blast not being executed

v1.4.11 bactopia/bactopia "Metamorph Ring" - 2020/09/19

Added

  • bactopia build checks if each environment is built before building
  • Can specify bactopia build to build a specific environment
  • Removed build numbers in Conda environment yamls
  • Created separate Conda yamls for Linux and Mac
  • NCBI assembly accessions will retrieve the most current version (e.g. .1, .2, .3, etc...)

Fixed

  • bactopia datasets trailing whitespace in species names
  • bactopia datasets random subsample missing specified species when --limit and --include_genus used
  • GitLab CI OSX compatibility
  • Adaptive resource allocations
  • Datasets are checked for existence
  • Variant calls against references with multiple chromosomes

v1.4.10 bactopia/bactopia "Jelly Ring" - 2020/08/25

Added

  • card is back as a default Ariba dataset
  • Added timestamps to versions files

Fixed

  • bactopia search not creating --outdir
  • gtdb tool not using prefix in outdir naming
  • pirate tool using pangenome alignment instead of core
  • Use of scratch causing logs to fail

v1.4.9 bactopia/bactopia "Toreador's Ring" - 2020/08/23

Added

  • Support for multiple accession
    • bactopia search (SRA)
    • Bactopia Tools: fastani, mashtree, pirate, roary (Assembly)

Fixed

  • Undefined variable in mapping_query.sh
  • ENA API endpoint for bactopia search
  • Updated GTDB-TK to 1.3.0 to support latest downloads
  • FastANI tool merge_results in no longer a separate step
    • ANI is now one-to-many calculations
  • --reassemble misapplied

v1.4.8 bactopia/bactopia "Shikaree Ring" - 2020/08/20

Added

  • Versions are logged for Bactopia
  • STDOUT/STDERR logs are kept for each sample
    • can be skipped using --skip_logs

Fixed

  • Long sample names breaking Prokka annotation
  • Syntax errors in Bactopia tools
  • null values being tested as integers
  • Ariba card and mlst downloads not working
  • missing parameter in GTDB Bactopia tool

v1.4.7 bactopia/bactopia "Serket Ring" - 2020/08/17

Added

  • --no_cache to skip caching ncbi assembly info

v1.4.6 bactopia/bactopia "Astral Ring" - 2020/08/17

Added

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

v1.4.5 bactopia/bactopia "Bomb Queen Ring" - 2020/08/13

Fixed

  • --min_basepairs and --min_reads not being honored

v1.4.4 bactopia/bactopia "Vilma's Ring" - 2020/08/13

Fixed

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

v1.4.3 bactopia/bactopia "Sattva Ring" - 2020/08/13

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

v1.4.2 bactopia/bactopia "Tamas Ring" - 2020/08/10

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

v1.4.1 bactopia/bactopia "Rajas Ring" - 2020/08/06

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

v1.4.0 bactopia/bactopia "Archer's Ring" - 2020/07/01

Added

  • New Bactopia Tools
    • eggnog for functional annotation using eggNOG-mapper
    • mashtree to create a tree using Mash distances
    • pirate to create pangenome using PIRATE
    • ismapper for insertion site discovery
    • Documentation for new tools and tweaks to existing
  • BTs roary and pirate can now be run on just completed genomes
  • Can limit number of completed genomes downloaded where applicable
  • bactopia datasets can provide list of RefSeq accessions to download
  • bactopia search can now use BioSample and Run accessions
  • bactopia search can select a subset of Experiments associated with a BioSample
  • Support for organisms with multiple MLST schemas
  • Assembly QC via QUAST and CheckM
  • Assemblies (local or NCBI Assembly accession) as inputs for Bactopia
  • Long reads as supplementary to paired end reads for hybrid assembly
  • Tools versions are locked to the minor version, not the patch

Fixed

  • summary will now determine absolute path of inputs
  • fastani improved user reference import
  • went back a version on call_variants openjdk version
  • all bactopia tools now put nextflow info in the same folder as outputs
  • Typos in docs
  • Bactopia Tools now check existence of include and exclude files
  • Lots more documentation
  • Updated citations/tools used by Bactopia
  • Did I mention typos?

Removed

  • ISMapper as part of the main pipeline (its now a tool)
  • insertion-sequences in bactopia datasets

v1.3.1 bactopia/bactopia "Emperor Hairpin" - 2020/04/20

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

v1.3.0 bactopia/bactopia "Leaping Boots" - 2020/02/19

Added

  • bactopia tools (BT) framework
    • docs for each tool
    • subcommand to execute tools bactopia tools
    • fastani - pairwise average nucleotide identity
    • gtdb - assigning objective taxonomic classifications
    • phyloflash - 16s assembly, alignment and tree
    • roary - pan-genome and core genome tree
    • summary - summary of results
  • --include and --exclude to modify which samples used in BT analysis
  • update-version.sh improvements
  • can now set how Nextflow publishes outputs (copy, symlink, etc...) via --publish_mode
  • Warning if output directory already exists and require --force to overwrite
  • option (--rfam) to turn on ncRNA annotation in Prokka
  • reduced "README.md" contents, instead point to documentation
  • Updated acknowledgements and bibtex for citations

Fixed

  • nextflow.config version out of sync
  • --available_datasets accessing not existent variable
  • --available_datasets is tested before requiring inputs
  • Make use of tbl2asn-forever
  • adjusted how Bactopia is executed, nextflow run no longer pulls from github

v1.2.4 bactopia/bactopia "Rabbit Charm" - 2019/12/20

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

v1.2.3 bactopia/bactopia "Tropical Punches +1" - 2019/12/19

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

v1.2.2 bactopia/bactopia "Tropical Punches" - 2019/10/22

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

v1.2.1 bactopia/bactopia "Fruit Punches" - 2019/10/17

Added

  • bactopia build to build Conda environments
  • Version info pulled from nextflow.config
  • Set default values resource allocations
  • Documentation on new changes
  • Automatic building of Conda environments, if none exist
  • --nfdir to determine where bactopia is being run from

Fixed

  • Never ending typos
  • --datasets now, not --dataset <-(Typo)
  • path for outputting Nextflow reports
  • Typo in antimicrobial_resistance.sh (task.cpus not cpus)
  • --species is now consistent between bactopia and bactopia datasets
  • Bug when checking if specific species dataset exists, but no species datasets exist
  • Cleaned up version update script
  • Cleaned up usage

Removed

  • --max_cpus ability to limit total cores used, access to config is being deprecated in Nextflow
  • --max_cpus since it is redudant to --cpus now

v1.2.0 bactopia/bactopia "Beestinger" - 2019/10/16

Added

  • --compress to compress certain outputs, default uncompressed
  • Species name check in bactopia datasets
  • Use requests package instead of urllib3
  • Added bactopia search to query ENA for list of Illumina accessions
  • Documentation
    • Feedback edits
    • Output overview
    • Additional program acknowledgements
    • bibtex of citations
    • missing parameters to usage
    • info for --genome_size parameter
    • bactopia search usage
    • Workflow overview
  • blastdbcmd compatible seqid to assembly fasta
    • allows search for entries with sample name
  • Mask low coverage regions in consensus (subs only) fasta
  • Added --dry_run to build conda envs one at a time (prevent parallel issues)
  • Added Singularity recipes
  • Added SLURM config

Fixed

  • Never ending typos
  • bactopia datasets lowercase species names not found in MLST schemas
  • bactopia version no longer calls nextflow
  • SEQUENCE_TYPE channel groups FASTQ and assembly
  • MINMER_QUERY channel groups FASTQ and signature
  • Ariba MLST always running with --noclean
  • Bugs related --compress
  • Reduced size of per-base coverage outputs
  • Removed -parse_seqids from makeblastdb command, caused blast queries to fail
  • genomeCoverageBed failing on empty BAM files

Removed

  • --clean_cache function

v1.1.0 bactopia/bactopia "Wooden Sword +1" - 2019/09/19

Added

  • NCBI's amrfinder
  • Dockerfile for main bactopia install
  • Completed documentation!

Fixed

  • insertion_sequences inputs are not now grouped into single channel
  • Unintended FASTQ duplication via poor publishDir pattern

v1.0.1 bactopia/bactopia "Wooden Sword" - 2019/09/12

Added

  • README.md documentation

Fixed

  • call_variants_auto bug fixed
  • documentation
  • version numbers

v1.0.0 bactopia/bactopia "Wooden Sword" - 2019/09/04

  • Initial release of bactopia/bactopia