environment.yml

# You can use this file to create a conda environment for this pipeline:
#   conda env create -f environment.yml
name: nf-core-mag-1.1.0
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - conda-forge::python=3.6.7 # 3.7.x conflicts with Nanolyse
  - conda-forge::markdown=3.1.1
  - conda-forge::pymdown-extensions=6.0
  - conda-forge::pygments=2.5.2
  - bioconda::fastqc=0.11.8
  - bioconda::multiqc=1.9
  - bioconda::fastp=0.20.0
  - bioconda::megahit=1.2.7
  - bioconda::metabat2=2.15
  - bioconda::samtools=1.9
  - bioconda::bowtie2=2.3.5
  - bioconda::quast=5.0.2
  - bioconda::prodigal=2.6.3
  - bioconda::diamond=0.9.24 # 0.9.25 conflicted with Busco over boost
  - conda-forge::r=3.6
  - conda-forge::biopython=1.74
  - bioconda::krona=2.7.1
  - conda-forge::r-markdown=1.0
  - conda-forge::r-ggplot2=3.2.0
  - bioconda::nanoplot=1.26.3
  - bioconda::filtlong=0.2.0
  - bioconda::porechop=0.2.3_seqan2.1.1
  - bioconda::nanolyse=1.1.0
  - bioconda::spades=3.13.1
  - bioconda::centrifuge=1.0.4_beta
  - bioconda::cat=4.6
  - bioconda::kraken2=2.0.8_beta