sfprov 0.1.0

Extract and store workflow provenance from RO-Crate and Nextflow DAG files.

sfprov — Workflow Provenance Parser

Extract, store, and query provenance from Nextflow pipelines into Neo4j.

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Install

pip install sfprov                 # core
pip install sfprov[opensearch]     # + OpenSearch indexing
pip install sfprov[extractors]     # + file feature extraction
pip install sfprov[all]            # everything

System dependencies (must be on PATH):

Format	Tool
SAM / BAM / CRAM	samtools
VCF / BCF	bcftools

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Quick Start

# 1. Initialise (starts Neo4j, writes nextflow.config)
sfprov init

# 2. Run your Nextflow pipeline as usual
nextflow run main.nf

# 3. Ingest provenance
sfprov ingest --ro-crate ./results/provenance/ro-crate-metadata.json \
              --lineage  ./work

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CLI

Command	Description
sfprov init	Bootstrap services and configure Nextflow
sfprov ingest	Parse and load provenance into Neo4j
sfprov parse	Parse only (no write)
sfprov status	Check service health
sfprov query	Run canned graph queries

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Requirements

• Python ≥ 3.10
• Docker + Compose V2
• Nextflow ≥ 23 with nf-prov plugin (configured automatically by sfprov init)