repo2rocrate

What it is and what it does

repo2rocrate is a command-line tool and Python API for converting workflow repositories into RO-Crate metadata packages. It targets repositories that follow best-practices guidelines from the Galaxy, Nextflow, and Snakemake communities, extracting metadata from known files and repository structure to populate an RO-Crate automatically. The tool can either add metadata in-place to an existing repository or build a complete RO-Crate in a separate directory, with options to override or supplement auto-detected values.

The package depends on click for CLI handling, pyyaml for configuration, and rocrate for RO-Crate generation. It's designed for researchers and workflow developers who need to package workflows with standardized, machine-readable metadata for reproducibility and FAIR data principles. The tool assumes repositories follow established community structure conventions; custom or non-standard layouts may require manual metadata additions.

Use it for:

• Convert a Galaxy workflow repository to an RO-Crate for submission to workflow registries or archives.
• Generate standardized metadata for a Nextflow nf-core pipeline to improve discoverability and reproducibility.
• Package a Snakemake workflow with RO-Crate metadata for sharing and citation in scientific publications.
• Batch-process multiple workflow repositories to ensure consistent metadata across a project or organization.
• Create machine-readable workflow documentation that integrates with workflow testing and monitoring platforms.

Worth the install?

AI-flagged interpretation of the facts on this page — verify before relying

Generates RO-Crate metadata from workflow repositories following best-practices guidelines for Galaxy, Nextflow, and Snakemake, either in-place or in a separate directory.

Yes, if you maintain Galaxy, Nextflow, or Snakemake workflows and need to generate RO-Crate metadata following community best-practices. Install with caution if your workflows deviate significantly from standard repository layouts, as the tool relies on known file structures. The aging maintenance status (no updates since May 2023) means compatibility with recent ecosystem changes is unverified; check whether your workflow language version is still supported.

Install

repo2rocrate on PyPI

pip install repo2rocrate

uv add repo2rocrate

poetry add repo2rocrate

Installing repo2rocrate

Before you install

Low install friction with three lightweight dependencies (click, pyyaml, rocrate). Maintenance status is aging—last release was in 2023 and no updates since, though the repository remains active and unarchived.

License in practice

Apache-2.0 is permissive and poses no restrictions on use, modification, or distribution in proprietary or open-source contexts.

Quickstart

pip install repo2rocrate

# Command-line usage
repo2rocrate -r /path/to/workflow-repo --repo-url https://github.com/user/repo --license GPL-3.0

# Or in a workflow directory
cd /path/to/workflow
repo2rocrate

Verify before relying

• Whether the package handles all edge cases in Galaxy, Nextflow, and Snakemake repository structures or only common layouts.
• Current compatibility with recent versions of Galaxy, Nextflow, and Snakemake ecosystem changes since 2023.
• Whether the rocrate dependency has received updates that may affect metadata generation quality.

Package facts

Evidence: repo2rocrate-0.1.2-py3-none-any.whl

Tags

More Scientific/Engineering packages