environment.yml

# You can use this file to create a conda environment for this pipeline:
#   conda env create -f environment.yml
name: nf-core-sicilian-1.0dev
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - conda-forge::python=3.6.13
  # - conda-forge::markdown=3.1.1
  # - conda-forge::pymdown-extensions=6.0
  # - conda-forge::pygments=2.5.2
  # TODO nf-core: Add required software dependencies here
  - conda-forge::numpy=1.19.5
  - conda-forge::pandas=1.1.5
  - conda-forge::pyarrow=4.0.0
  - bioconda::pysam=0.16.0.1
  - bioconda::samtools=1.12
  - conda-forge::gawk=5.1.0
  - bioconda::star=2.7.5a 
  - conda-forge::tqdm=4.61.0
  # R dependencies
  - bioconda::bioconductor-genomicalignments=1.22.0
  - conda-forge::r-tidyverse=1.3.1
  - conda-forge::r-glmnet=4.1
  - conda-forge::r-tictoc=1.0
  - dloewenstein::r-cutpointr=1.0.0
  - conda-forge::r-data.table=1.14.0