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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 YAML configuration 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.

note

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"
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