Conda support has landed!

  • Paolo Di Tommaso
  • 05 June 2018

Nextflow aims to ease the development of large scale, reproducible workflows allowing
developers to focus on the main application logic and to rely on best community tools and best practices.

For this reason we are very excited to announce that the latest Nextflow version (0.30.0) finally provides built-in support for Conda.

Conda is a popular package manager that simplifies the installation of software packages and the configuration of complex software environments. Above all, it provides access to large tool and software package collections maintained by domain specific communities such as Bioconda and BioBuild.

The native integration with Nextflow allows researchers to develop workflow applications in a rapid and easy repeatable manner, reusing community tools, whilst taking advantage of the configuration flexibility, portability and scalability provided by Nextflow.

How it works

Nextflow automatically creates and activates the Conda environment(s) given the dependencies specified by each process.

Dependencies are specified by using the conda directive, providing either the names of the required Conda packages, the path of a Conda environment yaml file or the path of an existing Conda environment directory.

Conda environments are stored on the file system. By default Nextflow instructs Conda to save the required environments in the pipeline work directory. You can specify the directory where the Conda environments are stored using the conda.cacheDir configuration property.

Use Conda package names

The simplest way to use one or more Conda packages consists in specifying their names using the conda directive. Multiple package names can be specified by separating them with a space. For example:

process foo {
    conda "bwa samtools multiqc"

    """
    your_command --here
    """
}

Using the above definition a Conda environment that includes BWA, Samtools and MultiQC tools is created and activated when the process is executed.

The usual Conda package syntax and naming conventions can be used. The version of a package can be specified after the package name as shown here: bwa=0.7.15.

The name of the channel where a package is located can be specified prefixing the package with the channel name as shown here: bioconda::bwa=0.7.15.

Use Conda environment files

When working in a project requiring a large number of dependencies it can be more convenient to consolidate all required tools using a Conda environment file. This is a file that lists the required packages and channels, structured using the YAML format. For example:

name: my-env
channels:
  - bioconda
  - conda-forge
  - defaults
dependencies:
  - star=2.5.4a
  - bwa=0.7.15

The path of the environment file can be specified using the conda directive:

process foo {
  conda '/some/path/my-env.yaml'

  '''
  your_command --here
  '''
}

Note: the environment file name must end with a .yml or .yaml suffix otherwise it won't be properly recognized. Also relative paths are resolved against the workflow launching directory.

The suggested approach is to store the the Conda environment file in your project root directory and reference it in the nextflow.config directory using the baseDir variable as shown below:

process.conda = "$baseDir/my-env.yaml"

This guarantees that the environment paths is correctly resolved independently of the execution path.

See the documentation for more details on how to configure and use Conda environments in your Nextflow workflow.

Bonus!

This release includes also a better support for Biocontainers. So far, Nextflow users were able to use container images provided by the Biocontainers community. However, it was not possible to collect process metrics and runtime statistics within those images due to the usage of a legacy version of the ps system tool that is not compatible with the one expected by Nextflow.

The latest version of Nextflow does not require the ps tool any more to fetch execution metrics and runtime statistics, therefore this information is collected and correctly reported when using Biocontainers images.

Conclusion

We are very excited by this new feature bringing the ability to use popular Conda tool collections, such as Bioconda, directly into Nextflow workflow applications.

Nextflow developers have now yet another option to transparently manage the dependencies in their workflows along with Environment Modules and containers technology, giving them great configuration flexibility.

The resulting workflow applications can easily be reconfigured and deployed across a range of different platforms choosing the best technology according to the requirements of the target system.

nextflow conda bioconda

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