1.6 KiB
1.6 KiB
Wave containers plugin for Nextflow
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'
}