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

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

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