README.md
August 7, 2026 · View on GitHub
A pipeline framework for Python
Documentation | ChangeLog | Examples | API
Why pipen?
pipen is designed for data scientists, bioinformaticians, and researchers who need to create reproducible, scalable computational pipelines without the complexity of traditional workflow systems.
Target Audience
- Data Scientists: Process large datasets with automatic parallelization and caching
- Bioinformaticians: Build reproducible analysis pipelines for genomics data
- Researchers: Create transparent, reproducible workflows for computational research
- DevOps Engineers: Orchestrate batch jobs across different schedulers (SLURM, SGE, Google Cloud)
Key Benefits
1. Zero Configuration
- Get started immediately with sensible defaults
- Configure only what you need, when you need it
- Profile-based configuration for different environments
2. Reproducibility Built-In
- Automatic job caching based on input/output signatures
- Full audit trail of pipeline runs and parameters
- Dependency tracking ensures processes run in correct order
3. Flexible Scheduling
- Run locally for development
- Scale to HPC clusters (SLURM, SGE)
- Deploy to cloud (Google Cloud Batch, SSH)
- Run in containers for reproducibility
4. Developer-Friendly
- Define pipelines as Python classes
- Use familiar Python syntax and tools
- Extensible plugin system for custom functionality
- Rich, informative logging and progress tracking
5. Data Flow Management
- Automatic data passing between pipeline stages
- Support for files, directories, and in-memory data
- Built-in operations for transforming and aggregating data
Comparison with Alternatives
| Feature | pipen | Snakemake | Nextflow | Airflow |
|---|---|---|---|---|
| Target Audience | Data Scientists, Bioinformaticians, Researchers, DevOps | Bioinformaticians | Bioinformaticians | Data Engineers |
| Learning Curve | Low | Medium | High | High |
| Python Integration | Native | Limited | Limited | Native |
| Scheduler Support | 6+ (Local, SGE, SLURM, SSH, Container, Gbatch) | Limited | Limited | Plugin-based |
| Caching | Built-in, automatic | Manual | Manual | Plugin-based |
| Cloud Native Support | Yes (Google Cloud Batch) | Partial | Yes | Yes |
| Interactive Debugging | Yes | Limited | No | No |
| Easy to Use | Define pipelines as Python classes, familiar syntax | Workflow DSL, separate config files | DAG definition in Python, complex UI | |
| Zero Configuration | Sensible defaults, configure only what needed | Many configuration options | Heavy configuration required | Complex setup |
| Nice Logging | Rich, informative, color-coded, progress bars | Text-based | Text-based | Basic logging |
| Highly Extensible | Simple plugin system, hook-based | Custom rules/scripts | Custom operators | Custom operators/providers |
| Data Flow Management | Built-in channel operations (expand_dir, collapse_files) | Manual handling | Channel system | XCom system |
| Reproducibility | Built-in caching, full audit trail | Manual | Versioned containers | DAG versioning |
| Flexible Scheduling | Switch schedulers without code changes | Config-based | Config-based | Config-based |
Installation
pip install -U pipen
Quickstart
example.py
from pipen import Proc, Pipen, run
class P1(Proc):
"""Sort input file"""
input = "infile"
input_data = ["/tmp/data.txt"]
output = "outfile:file:intermediate.txt"
script = "cat {{in.infile}} | sort > {{out.outfile}}"
class P2(Proc):
"""Paste line number"""
requires = P1
input = "infile:file"
output = "outfile:file:result.txt"
script = "paste <(seq 1 3) {{in.infile}} > {{out.outfile}}"
# class MyPipeline(Pipen):
# starts = P1
if __name__ == "__main__":
# MyPipeline().run()
run("MyPipeline", starts=P1)
> echo -e "3\n2\n1" > /tmp/data.txt
> python example.py
04-17 16:19:35 I core _____________________________________ __
04-17 16:19:35 I core ___ __ \___ _/__ __ \__ ____/__ | / /
04-17 16:19:35 I core __ /_/ /__ / __ /_/ /_ __/ __ |/ /
04-17 16:19:35 I core _ ____/__/ / _ ____/_ /___ _ /| /
04-17 16:19:35 I core /_/ /___/ /_/ /_____/ /_/ |_/
04-17 16:19:35 I core
04-17 16:19:35 I core version: 1.1.16
04-17 16:19:35 I core
04-17 16:19:35 I core ╔═══════════════════════════ MYPIPELINE ════════════════════════════╗
04-17 16:19:35 I core ║ My pipeline ║
04-17 16:19:35 I core ╚═══════════════════════════════════════════════════════════════════╝
04-17 16:19:35 I core plugins : verbose v1.1.1
04-17 16:19:35 I core # procs : 2
04-17 16:19:35 I core profile : default
04-17 16:19:35 I core outdir : /path/to/cwd/MyPipeline-output
04-17 16:19:35 I core cache : True
04-17 16:19:35 I core dirsig : 1
04-17 16:19:35 I core error_strategy : ignore
04-17 16:19:35 I core forks : 1
04-17 16:19:35 I core lang : bash
04-17 16:19:35 I core loglevel : info
04-17 16:19:35 I core num_retries : 3
04-17 16:19:35 I core scheduler : local
04-17 16:19:35 I core submission_batch: 8
04-17 16:19:35 I core template : liquid
04-17 16:19:35 I core workdir : /path/to/cwd/.pipen/MyPipeline
04-17 16:19:35 I core plugin_opts :
04-17 16:19:35 I core template_opts : filters={'realpath': <function realpath at 0x7fc3eba12...
04-17 16:19:35 I core : globals={'realpath': <function realpath at 0x7fc3eba12...
04-17 16:19:35 I core Initializing plugins ...
04-17 16:19:36 I core
04-17 16:19:36 I core ╭─────────────────────────────── P1 ────────────────────────────────╮
04-17 16:19:36 I core │ Sort input file │
04-17 16:19:36 I core ╰───────────────────────────────────────────────────────────────────╯
04-17 16:19:36 I core P1: Workdir: '/path/to/cwd/.pipen/MyPipeline/P1'
04-17 16:19:36 I core P1: <<< [START]
04-17 16:19:36 I core P1: >>> ['P2']
04-17 16:19:36 I verbose P1: in.infile: /tmp/data.txt
04-17 16:19:36 I verbose P1: out.outfile: /path/to/cwd/.pipen/MyPipeline/P1/0/output/intermediate.txt
04-17 16:19:38 I verbose P1: Time elapsed: 00:00:02.051s
04-17 16:19:38 I core
04-17 16:19:38 I core ╭═══════════════════════════════ P2 ════════════════════════════════╮
04-17 16:19:38 I core ║ Paste line number ║
04-17 16:19:38 I core ╰═══════════════════════════════════════════════════════════════════╯
04-17 16:19:38 I core P2: Workdir: '/path/to/cwd/.pipen/MyPipeline/P2'
04-17 16:19:38 I core P2: <<< ['P1']
04-17 16:19:38 I core P2: >>> [END]
04-17 16:19:38 I verbose P2: in.infile: /path/to/cwd/.pipen/MyPipeline/P1/0/output/intermediate.txt
04-17 16:19:38 I verbose P2: out.outfile: /path/to/cwd/MyPipeline-output/P2/result.txt
04-17 16:19:41 I verbose P2: Time elapsed: 00:00:02.051s
04-17 16:19:41 I core
MYPIPELINE: 100%|██████████████████████████████| 2/2 [00:06<00:00, 0.35 procs/s]
> cat ./MyPipeline-output/P2/result.txt
1 1
2 2
3 3
Examples
See more examples at examples/ and a more realcase example at:
https://github.com/pwwang/pipen-report/tree/master/example
Plugin gallery
Plugins make pipen even better.
pipen-annotate: Use docstring to annotate pipen processespipen-args: Command line argument parser for pipenpipen-board: Visualize configuration and running of pipen pipelines on the webpipen-diagram: Draw pipeline diagrams for pipenpipen-dry: Dry runner for pipen pipelinespipen-filters: Add a set of useful filters for pipen templates.pipen-lock: Process lock for pipen to prevent multiple runs at the same time.pipen-log2file: Save running logs to file for pipenpipen-poplog: Populate logs from jobs to running log of the pipelinepipen-report: Generate report for pipenpipen-runinfo: Save running information to file for pipenpipen-verbose: Add verbosal information in logs for pipen.pipen-email: Send email notification for pipeline status changes.pipen-gcs: A plugin for pipen to handle files in Google Cloud Storage.pipen-deprecated: A pipen plugin to mark processes as deprecated.pipen-mcp: A pipen plugin to turn pipen processes into MCP (model context protocol) processes.pipen-cli-init: A pipen CLI plugin to create a pipen project (pipeline)pipen-cli-ref: Make reference documentation for processespipen-cli-require: A pipen cli plugin check the requirements of a pipelinepipen-cli-run: A pipen cli plugin to run a process or a pipelinepipen-cli-gbatch: A pipen cli plugin to submit pipeline to Google Batch Jobs