# You can use this file to create a conda environment for this pipeline:
#   conda env create -f environment.yml
name: nf-core-methylseq-1.6.1
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  # nf-core dependencies
  - conda-forge::python=3.8.8
  - conda-forge::markdown=3.3.4
  - conda-forge::pymdown-extensions=8.1.1
  - conda-forge::pygments=2.8.1
  - conda-forge::pigz=2.6
  - bioconda::fastqc=0.11.9
  # Default Bismark pipeline
  - bioconda::trim-galore=0.6.6
  - bioconda::samtools=1.11
  - bioconda::bowtie2=2.4.2
  - bioconda::hisat2=2.2.1
  - bioconda::bismark=0.23.0
  - bioconda::qualimap=2.2.2d
  - bioconda::preseq=2.0.3
  - bioconda::multiqc=1.10.1
  # bwa-meth pipeline
  - bioconda::picard=2.25.4
  - bioconda::bwameth=0.2.2
  - bioconda::methyldackel=0.5.2