environment.yml

# You can use this file to create a conda environment for this pipeline:
#   conda env create -f environment.yml
name: ngs-preprocess-2.7
channels:
- conda-forge
- bioconda
- defaults
- anaconda
- r
dependencies:
## python pip dependencies
- pip
- pip:
  - biopython==1.78
  - jupyter
  - notebook==6.5.5
  - traitlets==5.9.0

## anaconda packages
- anaconda::hdf5
- anaconda::notebook

## conda-forge packages
- conda-forge::pigz=2.3.4 ## Required for TrimGalore multi-threading
- conda-forge::matplotlib=3.1.1
- conda-forge::gcc
- conda-forge::importlib_metadata

## bioconda packages
- bioconda::porechop=0.2.4
- bioconda::porechop_abi=0.5.0
- bioconda::fastp=0.23.2
- bioconda::samtools
- bioconda::bax2bam=0.0.9
- bioconda::pbtk=3.1.0
- bioconda::pbccs=6.4.0
- bioconda::lima=2.7.1
- bioconda::pbbam>=0.23.0
- bioconda::pycoqc=2.5.0.3
- bioconda::pysam
- bioconda::nanoqc=0.9.4
- bioconda::nanostat
- bioconda::nanoplot=1.41.0
- bioconda::nanofilt=2.8.0
- bioconda::sra-tools=3.0.3
- bioconda::entrez-direct=16.2
- bioconda::csvtk

## other
- plotly::plotly