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

https://github.com/bactopia/bactopia/assets/5334269/23c0314e-ffc8-424b-ac6e-04f9cdf8fb80

• 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

• 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

• 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

• 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