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Seqera Platform Tools

The Seqera tools provide comprehensive access to Seqera Platform for workflow management, compute environments, datasets, and Wave container provisioning. With 74+ tools available, this page highlights the most commonly used operations.

RAG search tools​

search_seqera_api​

Natural language search across all Seqera Platform, Wave, and SeqeraHub APIs. Use this to discover available operations.

Example prompts:

  • "How do I launch a workflow?"
  • "What APIs are available for managing compute environments?"
  • "Find tools for creating containers"
  • "Search for dataset management operations"

call_seqera_api​

Execute discovered APIs with validated parameters. Use after search_seqera_api to perform operations.

Example prompts:

  • "Call the API to list my workflows"
  • "Execute the container creation API"
  • "Run the workflow launch operation"

Workflow management​

platform_list_workflows​

List all workflow runs in a workspace with status, duration, and metadata.

Example prompts:

  • "List all my workflow runs"
  • "Show me the recent workflows in my workspace"
  • "What workflows have I run this week?"

platform_get_workflow​

Get detailed information about a specific workflow run including status, logs, and outputs.

Example prompts:

  • "Get details for workflow run 5abc123"
  • "Show me the status of my latest workflow"
  • "What's the output of workflow 12345?"

platform_launch_workflow​

Launch a new workflow run with specified parameters, compute environment, and configuration.

Example prompts:

  • "Launch nf-core/rnaseq with my sample sheet"
  • "Run the variant calling pipeline on AWS Batch"
  • "Start a new workflow with these parameters"

platform_cancel_workflow​

Cancel a running workflow.

Example prompts:

  • "Cancel workflow run 5abc123"
  • "Stop my currently running pipeline"

Compute environments​

platform_list_compute_envs​

List available compute environments in a workspace.

Example prompts:

  • "List my compute environments"
  • "What compute resources do I have available?"
  • "Show me the AWS Batch environments"

platform_get_compute_env​

Get detailed configuration for a compute environment.

Example prompts:

  • "Show details for compute environment aws-batch-prod"
  • "What's the configuration of my Kubernetes environment?"

platform_create_compute_env​

Create a new compute environment (AWS Batch, Google Cloud, Azure, Kubernetes, etc.).

Example prompts:

  • "Create an AWS Batch compute environment"
  • "Set up a new Kubernetes executor"
  • "Configure a Google Cloud environment for my pipelines"

Datasets​

platform_list_datasets​

List datasets available in a workspace.

Example prompts:

  • "List all datasets in my workspace"
  • "What datasets do I have available?"

platform_create_dataset​

Create a new dataset from a CSV/TSV file.

Example prompts:

  • "Create a dataset from my sample sheet"
  • "Upload this CSV as a new dataset"

Pipelines​

platform_list_pipelines​

List configured pipelines in a workspace.

Example prompts:

  • "List all pipelines in my workspace"
  • "What pipelines are available to run?"

platform_add_pipeline​

Add a new pipeline to the workspace.

Example prompts:

  • "Add nf-core/rnaseq to my workspace"
  • "Configure a new pipeline from GitHub"

Wave container service​

wave_get_container​

Create a container with specified packages (conda, pip) or from a Dockerfile.

Example prompts:

  • "Create a container with samtools and bwa"
  • "Build a container with Python 3.11 and pandas"
  • "Get a container with bioconda packages: salmon, kallisto"

wave_inspect_container​

Inspect a container image to see its layers, packages, and metadata.

Example prompts:

  • "Inspect the container image biocontainers/samtools"
  • "What packages are in this container?"

seqerahub_search_conda​

Search for conda packages across bioconda, conda-forge, and other channels.

Example prompts:

  • "Search for samtools in conda"
  • "Find bioinformatics packages for alignment"
  • "What versions of bwa are available?"

seqerahub_search_pypi​

Search for Python packages on PyPI.

Example prompts:

  • "Search for pandas on PyPI"
  • "Find Python packages for data visualization"

Organizations & Teams​

platform_list_organizations​

List organizations you belong to.

Example prompts:

  • "List my organizations"
  • "What organizations do I have access to?"

platform_list_workspaces​

List workspaces in an organization.

Example prompts:

  • "List workspaces in my organization"
  • "Show me all available workspaces"

platform_list_members​

List members of a workspace or organization.

Example prompts:

  • "Who are the members of this workspace?"
  • "List team members in my organization"

Example Session​

User: I want to run an RNA-seq analysis on my human samples

AI: Let me help you set that up. First, let me check your available resources.
    [Uses platform_list_compute_envs]

    You have these compute environments:
    - aws-batch-prod (AWS Batch, running)
    - local-docker (Local, running)

User: Use the AWS Batch one. I need a container with STAR and samtools

AI: [Uses wave_get_container with packages: star, samtools]
    Created container: wave.seqera.io/wt/abc123
    Contains: STAR 2.7.10b, samtools 1.17

User: Now launch nf-core/rnaseq with my samples

AI: [Uses platform_launch_workflow]
    Launched workflow run: 5x7abc123
    Pipeline: nf-core/rnaseq
    Compute: aws-batch-prod
    Status: SUBMITTED

User: What's the status?

AI: [Uses platform_get_workflow]
    Workflow: 5x7abc123
    Status: RUNNING
    Progress: 45% (18/40 tasks complete)
    Running for: 2h 15m

Workspace Context​

Most Platform operations require a workspace context. The AI assistant automatically uses your current workspace, or you can specify one:

Example prompts:

  • "List workflows in workspace 'production'"
  • "Switch to the 'development' workspace"
  • "Use organization 'my-lab' and workspace 'rnaseq-project'"