Summary

nf-gc is a Nextflow plugin for conservative, shallow garbage collection of workflow artifacts. It tracks successful non-cached task outputs owned by the Nextflow work directory and reclaims eligible intermediates after their producer becomes dependency-closed. When ownership or retention cannot be established safely, the artifact is kept.

Get Started

Enable the plugin in your pipeline nextflow.config:

plugins {
    id 'nf-gc@0.1.0'
}

Nextflow downloads the published plugin from the Nextflow Registry when the pipeline runs. No nf-gc-specific pipeline configuration is required.

nf-gc requires Nextflow 26.04.0 or newer.

Examples

Run any Nextflow pipeline with the plugin enabled, either from nextflow.config as above or from the command line:

nextflow run main.nf -plugins nf-gc@0.1.0

For repository development and the full regression suite:

./scripts/bootstrap-dev.sh
source env.sh
./test.sh

Eligible intermediate task outputs remain available until their producer process becomes dependency-closed. Publication-sensitive, terminal, cached, failed, external, or otherwise uncertain artifacts are retained conservatively.

Scope and Compatibility

• Minimum Nextflow version: 26.04.0.
• Validated development/runtime version: 26.04.6.
• Collection is shallow and limited to task outputs owned by the Nextflow work directory.
• Cached tasks, failed or unknown task states, terminal process outputs, and outputs outside task work ownership are kept.
• publishDir protection is artifact-level for pattern-selected outputs. For synchronous link-family publication, observed Nextflow publication events also resolve saveAs selection without re-running user closures; async saveAs, disabled publication, and otherwise ambiguous publication remain conservative.
• Any configured workflow output currently keeps intermediate task outputs for the run; artifact-level workflow-output provenance is not yet modelled.
• Staged external inputs are never acquired as owned artifacts. Re-emitted upstream artifacts are held until the relay dependency closes.
• Filesystem deletion does not follow symbolic links.
• Reclaimed artifacts are not guaranteed to remain available for a later -resume run.

The retention policy is intentionally conservative: uncertainty resolves to KEEP rather than DELETE.

Validation

The 0.1.0 behavior contract is covered by 43 functional regression cases against real Nextflow work directories and filesystem state. The plugin has also been integration-tested with nf-core/rnaseq 3.26.0 using its official test profile, including STAR/Salmon, QC, MultiQC, hard-link publication, and nf-core-style saveAs retention gates.

Contributing

• Contribution guide
• Reporting issues
• Testing
• Changelog

License

Licensed under the Apache License 2.0. See LICENSE for the full license text.