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YAML configuration

Seqerakit supports the creation and deletion of the following Seqera Platform resources, listed here with their respective Platform CLI resource names:

  • Pipeline actions: actions
  • Compute environments: compute-envs
  • Credentials: credentials
  • Datasets: datasets
  • Labels (including resource labels): labels
  • Pipeline launch: launch
  • Organization members: members
  • Organizations: organizations
  • Workspace and team participants: participants
  • Pipelines: pipelines
  • Pipeline secrets: secrets
  • Teams: teams
  • Workspaces: workspaces

To determine the options to provide as definitions in your YAML file, run the Platform CLI help command for the resource you want to create.

  1. Retrieve CLI options:

    Obtain a list of available CLI options for defining your YAML file with the Platform CLI help command. For example, to add a pipeline to your workspace, view the options for adding a pipeline:

    tw pipelines add -h
    Usage: tw pipelines add [OPTIONS] PIPELINE_URL

    Add a workspace pipeline.

    Parameters:
    *     PIPELINE_URL                         Nextflow pipeline URL.

    Options:
    * -n, --name=<name>                        Pipeline name.
      -w, --workspace=<workspace>              Workspace numeric identifier (TOWER_WORKSPACE_ID as default) or workspace reference as OrganizationName/WorkspaceName
      -d, --description=<description>          Pipeline description.
          --labels=<labels>[,<labels>...]      List of labels seperated by coma.
      -c, --compute-env=<computeEnv>           Compute environment name.
          --work-dir=<workDir>                 Path where the pipeline scratch data is stored.
      -p, --profile=<profile>[,<profile>...]   Comma-separated list of one or more configuration profile names you want to use for this pipeline execution.
          --params-file=<paramsFile>           Pipeline parameters in either JSON or YML format.
          --revision=<revision>                A valid repository commit Id, tag or branch name.
      ...

  2. Define key-value pairs in YAML:

    Translate each CLI option into a key-value pair in the YAML file. The structure of your YAML file should reflect the hierarchy and format of the CLI options. For example:

    pipelines:
      - name: 'my_first_pipeline'
        url: 'https://github.com/username/my_pipeline'
        workspace: 'my_organization/my_workspace'
        description: 'My test pipeline'
        labels: 'yeast,test_data'
        compute-env: 'my_compute_environment'
        work-dir: 's3://my_bucket'
        profile: 'test'
        params-file: '/path/to/params.yaml'
        revision: '1.0'

    In this example:

    • The keys (name, url, workspace, and so forth) are the keys derived from the CLI options.
    • The corresponding values are user-defined.

Best practices​

  • The indentation and structure of the YAML file must be correct — YAML is sensitive to formatting.
  • Use quotes around strings that contain special characters or spaces.
  • To list multiple values (such as multiple labels, instance-types, or allow-buckets), separate values with commas. This is shown with labels in the preceding example.
  • For complex configurations, see Templates.

Templates​

See Templates for YAML file templates for each of the entities that can be created in Seqera.

YAML Configuration Options​

Some options handled specially by seqerakit or not exposed as tw CLI options can be provided in your YAML configuration file.

Pipeline parameters using params and params-file​

To specify pipeline parameters, use params: to specify a list of parameters or params-file: to point to a parameters file.

For example, to specify pipeline parameters within your YAML:

params:
  outdir: 's3://path/to/outdir'
  fasta: 's3://path/to/reference.fasta'

To specify a file containing pipeline parameters:

params-file: '/path/to/my/parameters.yaml'

Or provide both:

params-file: '/path/to/my/parameters.yaml'
params:
  outdir: 's3://path/to/outdir'
  fasta: 's3://path/to/reference.fasta'
note

If duplicate parameters are provided, the parameters provided as key-value pairs inside the params nested dictionary of the YAML file will take precedence over values in the params-file.

Overwrite​

For every entity defined in your YAML file, specify overwrite: True to overwrite any existing Seqera entities of the same name.

Seqerakit will first check to see if the name of the entity exists. If so, it will invoke a tw <resource> delete command before attempting to create it based on the options defined in the YAML file.

DEBUG:root: Overwrite is set to 'True' for organizations

DEBUG:root: Running command: tw -o json organizations list
DEBUG:root: The attempted organizations resource already exists. Overwriting.

DEBUG:root: Running command: tw organizations delete --name $SEQERA_ORGANIZATION_NAME
DEBUG:root: Running command: tw organizations add --name $SEQERA_ORGANIZATION_NAME --full-name $SEQERA_ORGANIZATION_NAME --description 'Example of an organization'

Specify JSON configuration files with file-path​

The Platform CLI allows the export and import of entities through JSON configuration files for pipelines and compute environments. To use these files to add a pipeline or compute environment to a workspace, use the file-path key to specify a path to a JSON configuration file.

An example of the file-path option is provided in the compute-envs.yaml template:

compute-envs:
  - name: 'my_aws_compute_environment'                              # required
    workspace: 'my_organization/my_workspace'                       # required
    credentials: 'my_aws_credentials'                               # required
    wait: 'AVAILABLE'                                               # optional
    file-path: './compute-envs/my_aws_compute_environment.json'     # required
    overwrite: True
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