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Dependencies

Any workflow requires a set of dependencies. Nextflow gives a range of helper features to manage the dependency hell.

A simple workflow

To start practicing with Nextflow you can use a simple workflow:

  1. Gather the tools you need from bioconda creating an environment
  2. Experiment the pipeline with your environment
  3. When ready, export your environment as a yaml file
  4. Convert the environment to a container (Docker or Singularity)

In this way you can combine the convenience of a simple prototyping with the robustness of containers.

Converting an environment to a Singularity image

A definition file that is based on a YAML file makes it easy to immediately create an image just changing the YAML file.

Here an example of a definition file that will load a ./env.yaml file to be used to create the whole image modeled as a conda environment.

Bootstrap: docker
From: centos:centos7.6.1810

%files
    ./env.yaml /etc/env.yaml

%environment
    source /opt/software/conda/bin/activate /opt/software/conda_env


%post
    yum -y install epel-release wget which nano curl zlib-devel
    yum -y groupinstall "Development Tools"

    mkdir -p /opt/software

    cd /opt/software
    curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
    sh ./Miniconda3-latest-Linux-x86_64.sh -p /opt/software/conda -b

    /opt/software/conda/bin/conda config --add channels defaults
    /opt/software/conda/bin/conda config --add channels conda-forge
    /opt/software/conda/bin/conda config --add channels bioconda
    /opt/software/conda/bin/conda install -y -c conda-forge mamba
    ls -l /etc/*.yaml
    /opt/software/conda/bin/mamba env create -p /opt/software/conda_env  --file /etc/env.yaml
    source /opt/software/conda/bin/activate /opt/software/conda_env

    cd /opt/software

To build the image (.simg) from the definition file (.def):

sudo singularity build denovo.simg denovo.def

Converting an environment to a Docker image

A dockerfile is provided, that can be built with:

# We can call the image "denovo", tagging it as last version
sudo docker build -t denovo:latest .

# Test any tool like:
sudo docker run --rm denovo:latest abricate -h

A different approach: nf-core modules

DSL2 enabled a modular approach, and the "nf-core" organization curates a set of reusable modules.

The use of Bioconda packages enables the developers to specify the source of the tools from the module itself, for example if bwa is required:

    conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7' :
        'quay.io/biocontainers/bwa:0.7.17--hed695b0_7' }"