Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes. mSystems. 5 (2020)

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!

• 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

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

• 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

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

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