Secrets

New in version 22.10.0: Previewed in 21.09.0-edge.

Nextflow has built-in support for pipeline secrets to allow users to safely provide sensitive information to a pipeline execution.

How it works

This feature allows decoupling the use secrets in your pipelines from the pipeline code and configuration files. Secrets are instead managed by Nextflow and store separately into a local store only accessible to the secrets owner.

When the pipeline execution is launched Nextflow inject the secrets in pipeline jobs without leaking them into temporary execution files. The secrets are accessible into the job command via environment variables.

Command line

Nextflow provides a command named secrets. This command allows four simple operations:

list

List secrets available in the current store e.g. nextflow secrets list.

get

Retrieve a secret value e.g. nextflow secrets get FOO.

set

Create or update a secret e.g. nextflow secrets set FOO "Hello world"

delete

Delete a secret e.g. nextflow secrets delete FOO.

Configuration file

Once create the secrets can be used in the pipeline configuration file as implicit variables using the secrets scope:

aws {
  accessKey = secrets.MY_ACCESS_KEY
  secretKey = secrets.MY_SECRET_KEY
}

The above snippet access the secrets MY_ACCESS_KEY and MY_SECRET_KEY previously and assign them to the corresponding AWS credentials settings.

Warning

Secrets cannot be assigned to pipeline parameters.

Process directive

Secrets can be access by pipeline processes by using the secret directive. For example:

process someJob {
    secret 'MY_ACCESS_KEY'
    secret 'MY_SECRET_KEY'

    script:
    """
    your_command --access \$MY_ACCESS_KEY --secret \$MY_SECRET_KEY
    """
}

The above snippet runs a command in with the variables MY_ACCESS_KEY and MY_SECRET_KEY are injected in the process execution environment holding the values defines in the secret store.

Warning

The secrets are made available in the process context running the command script as environment variables. Therefore make sure to escape the variable name identifier with a backslash as shown in the example above, otherwise a variable with the same will be evaluated in the Nextflow script context instead of the command script.

Note

This feature is only available when using the local or grid executors (Slurm, Grid Engine, etc). The AWS Batch executor allows the use of secrets when deploying the pipeline execution via Seqera Platform.

Pipeline script

New in version 24.03.0-edge.

Secrets can be accessed in the pipeline script using the secrets variable. For example:

workflow.onComplete {
    println("The secret is: ${secrets.MY_SECRET}")
}

Note

This feature is only available when using the local or grid executors (Slurm, Grid Engine, etc). The AWS Batch executor allows the use of secrets when deploying the pipeline execution via Seqera Platform.