Workflow Gallery#
The Workflow Gallery is a curated collection of complete, validated example workflows that progress from fundamental concepts to production-grade bioinformatics pipelines. Every workflow in this gallery passes oxo-flow validate and demonstrates real CLI output.
Use this gallery to learn oxo-flow incrementally — each example builds on concepts from the previous one.
Learning Path#
| # | Workflow | Complexity | Concepts Covered |
|---|---|---|---|
| 01 | Hello World | ⭐ | Minimal rule, shell commands, output files |
| 02 | File Pipeline | ⭐⭐ | Multi-rule DAG, input/output chaining, config variables |
| 03 | Parallel Samples | ⭐⭐ | Wildcard expansion, fan-out/fan-in, resource declarations |
| 04 | Scatter-Gather | ⭐⭐⭐ | Data partitioning, parallel chunk processing, result merging |
| 05 | Environment Management | ⭐⭐⭐ | Per-rule conda, docker, and singularity environments |
| 06 | RNA-seq Quantification | ⭐⭐⭐⭐ | Complete transcriptomics pipeline, STAR, featureCounts, MultiQC |
| 07 | WGS Germline Calling | ⭐⭐⭐⭐⭐ | GATK best practices, BQSR, HaplotypeCaller, VEP annotation |
| 08 | Multi-Omics Integration | ⭐⭐⭐⭐⭐ | WGS + RNA-seq + Methylation, branching DAG, cross-omics integration |
Quick Start#
Every gallery workflow can be validated, inspected, and dry-run using the oxo-flow CLI:
# Validate a workflow
oxo-flow validate examples/gallery/01_hello_world.oxoflow
# Preview the execution plan
oxo-flow dry-run examples/gallery/02_file_pipeline.oxoflow
# Visualize the DAG
oxo-flow graph examples/gallery/06_rnaseq_quantification.oxoflow
# Lint for best practices
oxo-flow lint examples/gallery/07_wgs_germline.oxoflow
Skill Progression#
Beginner (Workflows 01–02)#
Learn the fundamental building blocks: rules, shell commands, inputs, outputs, and how oxo-flow resolves dependencies automatically from file paths.
Intermediate (Workflows 03–05)#
Master wildcards for multi-sample processing, scatter-gather parallelism patterns, and per-rule environment isolation with conda, docker, and singularity.
Advanced (Workflows 06–08)#
Build production-grade bioinformatics pipelines covering RNA-seq, whole-genome sequencing, and multi-omics integration with clinical-grade reporting and complex DAG topologies.
All Workflows Are Tested#
Every workflow in this gallery is validated as part of oxo-flow's continuous integration pipeline. The validation output shown in each page is the actual CLI output — not simulated.