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nf-core profiles

Config and 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.

Explore config files of rnaseq pipeline

  1. Find rnaseq workflow directory
  2. Display the config files present in workflow directory
    • nextflow.config and
    • conf/base.config
  3. Look at the merged config with the command nextflow config
Solution
  1. nextflow info nf-core /rnaseq
  2. The two files are accessible with :
    • more /home/$USER/.nextflow/assets/nf-core/rnaseq/nextflow.config
    • more /home/$USER/.nextflow/assets/nf-core/rnaseq/conf/base.config
  3. The merged config is visible with :
    • nextflow config nf-core/rnaseq

Profile genotoul

With the command nextflow run nf-core/rnaseq -profile genotoul, the profile genotoul.config will be automatically download and use.

Warning

This profile is only available with nf-core pipelines.

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

Info

Note that the order in which config profiles are specified matters. Their priority increases from left to right.

Profile test

The test profile is a bit of a special case. Whereas all other config profiles tell Nextflow how to run on different computational systems, the test profile configures each nf-core pipeline to run without any other command line flags. It specifies URLs for test data and all required parameters. Thanks to this, you can test any nf-core pipeline.

Test a pipeline with profile genotoul and test

The first thing to do before executing a pipeline on your own data is to try with test profile. 

nextflow run nf-core/rnaseq -profile test,genotoul --outdir results -r 3.14.0