Config profiles
Nextflow can load pipeline configurations from multiple locations. To make it easy to apply a group of options on the command line, Nextflow uses the concept of config profiles. nf-core pipelines load configuration in the following order:
- Pipeline: Default 'base' config
- Always loaded. Contains pipeline-specific parameters and "sensible defaults" for things like computational requirements
- Does not specify any method for software packaging. If nothing else is specified, Nextflow will expect all software to be available on the command line.
- Pipeline: Core config profiles
- All nf-core pipelines come with some generic config profiles. The most commonly used ones are for software packaging :
docker
,singularity
andconda
- Other core profiles are
awsbatch
,debug
andtest
- All nf-core pipelines come with some generic config profiles. The most commonly used ones are for software packaging :
- nf-core/configs: Server profiles
- At run time, nf-core pipelines fetch configuration profiles from the configs remote repository. The profiles here are specific to clusters at different institutions. Genotoul profile is available for nf-core pipelines.
- Local config files given to Nextflow with the
-c
flag - Command line configuration
Multiple comma-separated config profiles can be specified in one go, so the following commands are perfectly valid:
nextflow run nf-core/rnaseq -profile test,singularity
nextflow run nf-core/hlatyping -profile debug,genotoul
Note that the order in which config profiles are specified matters. Their priority increases from left to right.