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Pipelines

Pipelines are pre-configured workflows (Nextflow or WDL) available for execution on GCP Batch.

Available Pipelines

View available pipelines in the Compute service:

Pipelines

Or use the CLI:

iflow pipelines list

Output:

SLUG                      VERSION    NAME                      MODE
---------------------------------------------------------------------------------
hereditary-mock           1.0.0      Hereditary Mock Pipeline  direct_wdl
wdl-minimal               1.0.0      WDL Minimal Pipeline      direct_wdl
nextflow-minimal          1.0.0      nextflow-minimal          container_entrypoint
nfcore-demo               1.0.0      nf-core/demo              direct_nextflow

Pipeline Information

Each pipeline displays:

Field Description
Slug URL-safe identifier (e.g., hereditary-mock)
Version Semantic version (e.g., 1.0.0)
Name Human-readable name
Mode Execution type: direct_wdl, direct_nextflow, or container_entrypoint

Get details for a specific pipeline:

iflow pipelines info hereditary-mock

View inputs and outputs:

iflow pipelines describe hereditary-mock

Execution Modes

Mode Description Engine
direct_wdl WDL workflows executed via Cromwell Cromwell 86
direct_nextflow Nextflow pipelines executed directly Nextflow
container_entrypoint Custom container with entrypoint script Docker

Pipeline Versioning

Pipelines support semantic versioning. Multiple versions can coexist:

# List all versions of a pipeline
iflow pipelines versions hereditary-mock

# Use specific version
iflow analyses submit --pipeline hereditary-mock -V 1.0.0 --watch

Adding Custom Pipelines

Administrators can add custom pipelines from WDL or Nextflow URLs:

iflow pipelines add --url https://workflows.example.com/.../workflow.wdl

The system automatically:

  • Detects meta.json in the same directory
  • Extracts version, name, description
  • Parses input/output definitions

Use --force to update an existing pipeline version.

See CLI Pipelines Guide for details.

Running a Pipeline

  1. Click on a pipeline to view details
  2. Configure required parameters
  3. Click Launch to start execution

Or use the CLI:

iflow analyses submit --pipeline hereditary-mock \
  -P case_id=case-001 \
  -P child_fastq=data/R1.fastq.gz \
  --watch

See Running Workflows for detailed instructions.

Next Steps