Seqera Labs Showcase Automation Scripts

Overview

This repository contains automation scripts for launching and collecting information from pipelines in the Seqera Labs platform.

launch_pipelines.py

This script performs the following steps:

• Reads pipeline details from multiple YAML files in ./pipelines/.
• Reads compute environment details from multiple files in ./compute-envs/.
• Creates combinations of pipelines and compute environments in an all-by-all manner.
• Includes YAML files specified in include/ as both pipelines and compute environments.
• Excludes YAML files specified in exclude/ based on pipeline and compute environment names.
• Launches all pipelines generated from this data.
• Logs any "failure to launch" without causing the program to fail.
• Writes all pipelines to a YAML file for subsequent steps.

collect_metadata.py

This script performs the following steps:

• Uses the JSON from the previous step.
• Reads workspace and workflow ID from JSON produced in the first step.
• Utilizes tw runs dump to download relevant information.
• Creates a JSON file containing all pipeline run information.
• Sends a message to Slack (--slack) in the specified channel (--slack_channel) with the compressed JSON as an attachment.
• If --delete is enabled, it removes the pipeline if it has successfully completed.
• If --force is enabled, it removes the pipeline even if it has not finished or failed.

Input YAML Files

pipelines

Each entry in the YAML must specify a list of pipelines to launch, with the following fields:

• name (string): User-readable name of the launched workflow.
• url (string): The URL of the repository or pipeline name in the workspace.
• latest (bool): Pull the latest version specified by revision (required).
• profiles (List of strings): Profiles to apply to the pipeline run. Use an empty list to mean no profile.

Example:

pipelines:
  - name: hello
    url: hello
    latest: true
    profiles: []

compute-envs

Each entry in the YAML must specify an existing compute environment in the Seqera platform workspace, with the following fields:

• ref (string): User-readable name of the compute environment.
• name (string): The name of the compute environment in the Seqera platform.
• workdir (string): The work directory to use for the compute environment. A subdirectory will be created per pipeline run.
• workspace (string): The ID of the workspace the compute environment belongs to.

Example:

compute-envs:
  - ref: aws
    name: seqera_aws_ireland_fusionv2_nvme
    workdir: s3://seqeralabs-showcase
    workspace: '138659136604200'

include

This file is made of a list of complete configurations, each containing a pipeline and compute environment that match the above files.

Example:

include:
- pipeline:
    name: sentieon
    url: nf-sentieon
    latest: true
    profiles:
    - test
  compute_environment:
    ref: aws
    name: seqera_aws_ireland_fusionv2_nvme
    workdir: s3://seqeralabs-showcase
    workspace: '138659136604200'

exclude

This file removes pipeline and compute environment combinations. It has the same format as the include YAML but removes existing combinations before running. This is applied after the include YAML.

Automated Running

An implementation of these two steps in GitHub Actions is included in ./.github/workflows/seqera-showcase.yml. In this workflow, the first job (launch) launches the pipelines, and the subsequent job (clearup-and-delete) runs the second process after a pre-defined wait period, implemented via a GitHub Deployment Environment. It uses a GitHub Action artifact to transfer the JSON file between jobs.