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Documentation hub

Every page here is rendered from the repository: the README, the agent guide, the guides in docs/ and the contributor notes. A change to one of those files appears here on the next build.

README

A self-maintaining library of nf-core pipelines for AI agents and bioinformaticians. Each pipeline is an unmodified git submodule pinned to a release, with a generated skill.md that says how to run it and a reference.md that lists every parameter. The nfclaw…

README.md9 min read

Contributing

Contributions are welcome: new pipelines and handoff rules, runner features and fixes, tests and documentation. This page covers how to report a…

CONTRIBUTING.md10 min read

Agent guide

This repository is a library of nf-core pipelines. Each one lives in pipelines/<name>/: upstream/ holds the pinned pipeline code (a git submodule)…

AGENTS.md17 min read

Security policy

--- --- main Yes. Every fix lands here first. The latest release (v1.0.0) Yes. A security fix for it is released as a patch version (v1.0.1). Earlier…

SECURITY.md1 min read

Changelog

User-visible changes to nf-claw, newest first, by pull request. Each release is a tag vX.Y.Z on main with release notes. Pipeline releases the…

CHANGELOG.md15 min read

Notice & credits

nf-claw was created by Danilo Monge (Eberhard Karls Universität Tübingen) and is released under the MIT License (see LICENSE). THE PIPELINES ARE…

NOTICE1 min read

nf-claw architecture

How the repository and the nfclaw runner are put together. nf-claw takes its parameter documentation and its general input validation from each…

docs/architecture.md20 min read

Chaining pipelines

nfclaw chain run runs several nf-core pipelines in sequence, for example fetchngs → rnaseq → differentialabundance. Each stage starts only after the…

docs/chaining.md14 min read

Engine and version compatibility

nf-claw runs each nf-core pipeline unmodified, pinned to the commit of a release tag. What a pipeline needs at run time (Nextflow version, Java…

docs/compatibility.md8 min read

Prepare DRAMP for Funcscan 4.0.0

The pinned Funcscan release uses AMPcombi 3.0.0. Its DRAMP downloader passes pandas NaN values from missing sequence cells to a string regex and…

docs/dramp-reference.md3 min read

Known issues and troubleshooting

Symptoms and their fixes. Most failures at run time are either environment problems (host, network or paths, fixed with nfclaw run flags or host…

docs/known-issues.md86 min read

Publication policy for the maintenance workflows

What the daily update and the weekly discovery must show before they change main. Both prepare one candidate commit and hand it to the same gate and…

docs/maintenance.md4 min read

nf-claw over MCP

nfclaw mcp serves the nf-claw library and runner over stdin/stdout to any Model Context Protocol client: Claude Code, Codex, Antigravity, Hermes, MCP…

docs/mcp.md15 min read

Validation scope and samplesheet generation

What nfclaw checks before a pipeline starts, what it leaves to the pipeline, how it writes a samplesheet from data files and for which pipelines, and…

docs/preflight.md14 min read

Replaying and verifying runs

How a run's provenance bundle replays it, what that replay checks before and after Nextflow runs, and how nfclaw verify and nfclaw assess compare a…

docs/replay.md10 min read

Scientific output contracts

nfclaw assess checks a run's outputs against expectations written down in a contract. It prints JSON and exits non-zero if any declared file, sample…

docs/scientific-output-contracts.md6 min read

Recorded workflow-source corrections

Three pinned releases need source changes that a process configuration cannot supply. nfclaw applies them to an independently copied working source…

docs/source-corrections.md5 min read

Timeouts, long analyses and monitoring

nfclaw run and nfclaw chain run have no overall time limit by default. Nothing cancels a run because it is slow or quiet: an analysis may spend hours…

docs/timeouts.md4 min read

Updating and discovery

How nf-claw follows nf-core releases. Two scheduled workflows bump the pins to new releases and add new pipelines, and a drift gate checks that the…

docs/updating.md5 min read

End-to-end validation

Every pipeline pinned at the time of the validation was attempted through nfclaw. Of 91 bundled tests, 90 reached success, including proteinfold's…

docs/validation.md64 min read