# 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