# scipipe/scipipe

Robust, flexible and resource-efficient pipelines using Go and the commandline

Repository: https://github.com/scipipe/scipipe
Canonical: https://ross.abutalabs.com/products/scipipe
Homepage: https://scipipe.org
Language: Go
License: MIT
License Family: permissive
Topics: scientific-workflows, bioinformatics-pipeline, workflow, go, dataflow, pipeline, cheminformatics, bioinformatics, fbp, scipipe, workflow-engine, golang
Last push: 2024-08-14T01:44:15+00:00

## Health v2 (maintenance only)
Score: 23/100 (v2, computed 2026-09-03T02:20:16.233290+00:00)
- activity 0, release rhythm 8, longevity 100
- inputs: {"age_days": 4197, "days_push": 750, "days_rel": null, "gap_med": null, "n_releases_24m": 0}
- flags: none
- formula: round(0.45*activity + 0.35*rhythm + 0.20*longevity); archived -> min(score, 10)

## Adoption (not part of the score)
Stars 1109, forks 74 (observed 2026-08-28T04:03:37.328014+00:00)

## What it is
SciPipe is a Go library for writing scientific workflows (pipelines) based on Flow-Based Programming, wrapping command-line tools and Go code into networks of channels and processes. Workflows compile to fast, self-contained binaries with task parallelism, streaming, restartability, and audit/provenance reports.

## Use cases
- build bioinformatics pipelines in Go
- chain command-line tools into reproducible workflows
- run many dependent programs in parallel on multiple cores
- stream data between pipeline steps to save disk space
- resume an interrupted workflow run without overwriting outputs
- generate audit reports for scientific workflow provenance
- build cheminformatics data processing pipelines

## When to choose
- you want workflows as compiled, portable Go binaries
- you need to wrap arbitrary command-line tools in a pipeline
- you need task and pipeline parallelism with streaming support
- you want provenance/audit reports and restartable runs
- you prefer writing pipelines in Go code rather than YAML

## When to avoid
- you need a large ecosystem of prebuilt workflow steps or community recipes
- you prefer declarative YAML/DSL workflow definitions like Snakemake or Nextflow
- you need container scheduling or cluster orchestration built in
- your team does not work in Go

## Facets
- artifact type: library
- maturity: maintenance
- function: workflow-automation, cli, concurrency, developer-tools
- domain: bioinformatics, developer-tools
- platform: go, cross-platform, cli
- tags: scientific-workflows, flow-based-programming, bioinformatics-pipeline, cheminformatics, dataflow, provenance, reproducibility, pipeline-parallelism, data-engineering, automation, command-line, linux, macos

## Member repositories
- scipipe/scipipe (main) score 23

## Provenance
- Observed fields: from GitHub, fetched 2026-08-28T04:03:37.328014+00:00.
- Health v2: computed from the inputs above; adoption is never an input.
- Inferred fields (summary, facets, guidance): AI-extracted, prompt v1, taxonomy v1, on 2026-08-30T06:43:37.613598+00:00, confidence not recorded.
  - readme: https://github.com/scipipe/scipipe (fetched 2026-08-28T04:03:37.328014+00:00, sha 533098252fec)
  - homepage: https://scipipe.org (fetched 2026-08-29T12:47:12.181799+00:00, sha d64551e183a1)
  - site_page: https://scipipe.org/install (fetched 2026-08-29T12:47:12.191752+00:00, sha efdd920937ea)
- Data as of 2026-08-30T08:39:29.467469+00:00.