Conda environments¶
Conda is an open source package and environment management system that simplifies the installation and the configuration of complex software packages in a platform agnostic manner.
Nextflow has built-in support for Conda that allows the configuration of workflow dependencies using Conda recipes and environment files.
This allows Nextflow applications to use popular tool collections such as Bioconda whilst taking advantage of the configuration flexibility provided by Nextflow.
Prerequisites¶
This feature requires Nextflow version 0.30.x or higher and the Conda or Miniconda package manager installed on your system.
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.
Note
Conda environments are stored on the file system. By default Nextflow instructs Conda to save the required environments in the pipeline work directory. Therefore the same environment can be created/saved multiple times across multiple executions when using a different work directory.
You can specify the directory where the Conda environments are stored using the conda.cacheDir
configuration property (see the configuration page for details).
When using a computing cluster, make sure to use a shared file system path
accessible from all computing nodes.
Warning
The Conda environment feature is not supported by executors which use a remote object storage as a work directory eg. AWS Batch.
Use Conda package names¶
Conda package names can specified using the conda directive. Multiple package names can be specified
by separating them with a blank 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¶
Conda environments can also be defined using one or more Conda environment files. 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
Read the Conda documentation for more details about how to create environment files.
The path of an environment file can be specified using the conda directive:
process foo {
conda '/some/path/my-env.yaml'
'''
your_command --here
'''
}
Warning
The environment file name must end with a .yml or .yaml suffix otherwise
it won’t be properly recognised.
Alternatively it is also possible to provide the dependencies using a plain text file, just listing each package name as a separate line. For example:
bioconda::star=2.5.4a
bioconda::bwa=0.7.15
bioconda::multiqc=1.4
Note
Like before the extension matter, make sure such file ends with the .txt extension.
Use existing Conda environments¶
If you already have a local Conda environment, you can use it in your workflow specifying the
installation directory of such environment by using the conda directive:
process foo {
conda '/path/to/an/existing/env/directory'
'''
your_command --here
'''
}