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:

  1. 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.
  2. 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 and conda
    • Other core profiles are awsbatch, debug and test
  3. 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.
  4. Local config files given to Nextflow with the -c flag
  5. Command line configuration

image

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.

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