Quickstart

Follow these steps to convert your first workflow.

Basic Conversion

Example: Snakemake → DAGMan

wf2wf convert -i Snakefile -o pipeline.dag --report-md

  • -i / --input – source workflow

  • -o / --output – destination file

  • --report-md – generate a Markdown conversion report

Example: CWL → Nextflow with loss check

wf2wf convert -i analysis.cwl -o main.nf \
             --out-format nextflow \
             --fail-on-loss

Interactive Conversion

Interactive Resource Specification

# Convert with interactive mode for guided assistance
wf2wf convert -i workflow.smk -o workflow.dag --interactive

# This will prompt you for:
# - Missing resource specifications (CPU, memory, disk)
# - Container/environment requirements
# - Error handling configurations
# - File transfer mode optimization

Example Interactive Session

$ wf2wf convert -i workflow.smk -o workflow.dag --interactive

Found 3 tasks without explicit resource requirements.
Distributed systems require explicit resource allocation.
Add default resource specifications? [Y/n]: Y

Applied default resources: CPU=1, Memory=2048MB, Disk=4096MB

Found 2 tasks without container specifications.
Distributed systems typically require explicit environment isolation.
Add container specifications? [Y/n]: Y

Enable --auto-env to automatically build containers for these tasks.

Advanced Features

Resource Processing

# Convert with automatic resource inference and validation
wf2wf convert -i workflow.smk -o workflow.dag \
    --infer-resources \
    --validate-resources \
    --resource-profile cluster

Comprehensive Conversion

# Full-featured conversion with all enhancements
wf2wf convert -i workflow.smk -o workflow.dag \
    --interactive \
    --infer-resources \
    --validate-resources \
    --resource-profile cluster \
    --target-env distributed \
    --report-md \
    --verbose

Next Steps

  1. Try Interactive Mode: Use --interactive for guided conversions

  2. Explore Resource Features: Use --infer-resources and --validate-resources

  3. Review Loss Reports: Use --report-md to understand conversion implications

  4. Check Documentation: See Shared Infrastructure for detailed features

See the Commands page for full CLI reference.