Commands

Use the --help or -h option to list available commands and options:

seqerakit --help

Input

Seqerakit supports input through paths to YAML configuration files or directly from standard input (stdin).

• Using file path:

  seqerakit file.yaml

• Using stdin:

  cat file.yaml | seqerakit -

See Define your YAML file using CLI options for guidance on formatting your input YAML files.

Dryrun

Confirm that your configuration and command are correct before creating resources in your Seqera account, particularly when automating the end-to-end creation of multiple entities at once. To print the commands that would be executed with Platform CLI when using a YAML file, run your seqerakit command with the --dryrun option:

seqerakit file.yaml --dryrun

Specify targets

When using a YAML file as an input that defines multiple resources, use the --targets option to specify which resources to create. This option accepts a comma-separated list of resource names.

Supported resource names include:

• actions
• compute-envs
• credentials
• datasets
• labels
• launch
• members
• organizations
• participants
• pipelines
• secrets
• teams
• workspaces

For example, given a test.yaml file that defines the following resources:

workspaces:
  - name: 'workspace-1'
    organization: 'seqerakit'
...
compute-envs:
  - name: 'compute-env'
    type: 'aws-batch forge'
    workspace: 'seqerakit/workspace-1'
...
pipelines:
  - name: 'hello-world'
    url: 'https://github.com/nextflow-io/hello'
    workspace: 'seqerakit/workspace-1'
    compute-env: 'compute-env'
...

You can target the creation of pipelines only by running:

seqerakit test.yaml --targets pipelines

This command will create only the pipelines defined in the YAML file and ignore workspaces and compute-envs.

To create both workspaces and pipelines, run:

seqerakit test.yaml --targets workspaces,pipelines

Delete resources

Instead of adding or creating resources, specify the --delete option to recursively delete resources in your YAML file:

seqerakit file.yaml --delete

For example, if you have a file.yaml that defines an organization, workspace, team, credentials, and compute environment that have already been created, run seqerakit file.yaml --delete to recursively delete the same resources.

Use tw-specific CLI options

Specify tw-specific CLI options with the --cli= option:

seqerakit file.yaml --cli="--arg1 --arg2"

See CLI commands or run tw -h for the full list of options.

The --verbose option for tw CLI is currently not supported in seqerakit commands.

Example: HTTP-only connections

The Platform CLI expects to connect to a Seqera instance that is secured by a TLS certificate. If your Seqera Enterprise instance does not present a certificate, you must run your tw commands with the --insecure option.

To use tw-specific CLI options such as --insecure, use the --cli= option, followed by the options to use enclosed in double quotes:

seqerakit file.yaml --cli="--insecure"