Installation

Dependencies

This pipeline Nextflow requires Docker, Singularity or conda to run. Please read the information about how to proper choose between conda, docker and singularity profiles.

  1. Installing Nextflow

    curl -s https://get.nextflow.io | bash
    
  2. Download the pipeline

    nextflow pull fmalmeida/ngs-preprocess
    
  3. Test your installation

    nextflow run fmalmeida/ngs-preprocess --help
    
  4. Download required tools

    # for docker
    docker pull fmalmeida/ngs-preprocess:v2.5
    nextflow run fmalmeida/ngs-preprocess -profile docker [options]
    
    # for singularity
    # remember to properly set NXF_SINGULARITY_LIBRARYDIR
    # read more at https://www.nextflow.io/docs/latest/singularity.html#singularity-docker-hub
    export NXF_SINGULARITY_LIBRARYDIR=MY_SINGULARITY_IMAGES    # your singularity storage dir
    export NXF_SINGULARITY_CACHEDIR=MY_SINGULARITY_CACHE       # your singularity cache dir
    singularity pull \
          --dir $NXF_SINGULARITY_LIBRARYDIR \
          fmalmeida-ngs-preprocess-v2.5.img docker://fmalmeida/ngs-preprocess:v2.5
    nextflow run fmalmeida/ngs-preprocess -profile singularity [options]
    
    # for conda
    wget https://github.com/fmalmeida/ngs-preprocess/raw/master/environment.yml
    conda env create -f environment.yml # advice: use mamba
    nextflow run fmalmeida/ngs-preprocess -profile conda [options]
    
  5. (Optional) Install nf-core

    pip install nf-core>=1.10

Note

Now, everything is set up and ready to run. Remember to always keep your Docker images up to date (Docker pull will always download the latest).