environment.yml

# You can use this file to create a conda environment for this pipeline:
#   conda env create -f environment.yml
name: bacterial_wgs_training
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  ## conda-forge packages
  - conda-forge::python
  - conda-forge::r-base
  - conda-forge::r-optparse
  - conda-forge::r-tidyr
  - conda-forge::r-tidyverse
  - conda-forge::r-ggplot2
  - conda-forge::r-reshape2
  - conda-forge::r-viridis

  ## bioconda packages
  ## common
  - bioconda::fastqc
  - bioconda::fastp
  - bioconda::samtools
  - bioconda::bedtools
  - bioconda::multiqc
  - bioconda::bwa
  - bioconda::picard
  - bioconda::bcftools
  - bioconda::kraken2
  - bioconda::unicycler
  - bioconda::quast
  - bioconda::prokka
  - bioconda::taranis
  - bioconda::plasmidid
  - bioconda::gubbins
  - bioconda::snippy
  - bioconda::iqtree