environment.yml

# Whenever this file is updated, you need to run:
#
#   conda-lock -f environment.yml -p linux-64 -p osx-64 --filename-template "environment.{platform}.lock"
#
# This updates the environment.{platform}.lock files. conda-lock is avialable from
# pip (`pip install conda-lock`) or conda (`conda install conda-lock -c conda-forge`).
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - nomkl
  - python=3.6
  - dataclasses  # remove when minimum Python version is raised to 3.7
  - bowtie2>=2.4.2
  - bwa
  - minimap2
  - pysam
  - cutadapt=2.5
  - hapcut2=1.3.2
  - samtools
  - snakemake-minimal>=5.32.0,<6.5  # >=6.5 does not utilize all available cores.
  - starcode
  - tqdm
  - importlib_resources  # remove when minimum Python version is raised to 3.7
  - freebayes
  - ruamel.yaml
  - vcflib
  - ema=0.6.2
  - fastqc
  - multiqc>=1.10,<1.12
  - bcftools
  - gatk4
  - pandas
  - numpy
  - matplotlib-base>=3.0
  - picard-slim
  - dnaio
  - whatshap
  - mosdepth>=0.2.9
  - parallel 
  - pip