Summary

The Wave containers plugin provides integration with the Wave container service for dynamic container building, augmentation, and on-demand software provisioning.

Get Started

To use this plugin, add it to your nextflow.config:

plugins {
    id 'nf-wave'
}

Enable Wave in your configuration:

wave {
    enabled = true
}

Wave automatically builds containers from Conda packages or Dockerfiles defined in your processes.

Examples

Basic Wave configuration

plugins {
    id 'nf-wave'
}

wave {
    enabled = true
}

process {
    conda = 'samtools=1.17'
}

Using Wave with Conda packages

wave {
    enabled = true
}

process ALIGN {
    conda 'bioconda::bwa=0.7.17 bioconda::samtools=1.17'

    script:
    '''
    bwa mem ref.fa reads.fq | samtools view -bS - > aligned.bam
    '''
}

Wave with Fusion file system

wave {
    enabled = true
}

fusion {
    enabled = true
}

process.executor = 'awsbatch'
workDir = 's3://my-bucket/work'

Container augmentation

wave {
    enabled = true
    strategy = 'conda,container'
}

process TOOL {
    container 'ubuntu:22.04'
    conda 'bioconda::samtools=1.17'

    script:
    '''
    samtools --version
    '''
}

Using private registries

wave {
    enabled = true
}

docker {
    registry = 'quay.io'
}

License

Apache License 2.0