sfprov — Workflow Provenance Parser
Extract, store, and query provenance from Nextflow pipelines into Neo4j.
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 |
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
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 |
Requirements
- Python ≥ 3.10
- Docker + Compose V2
- Nextflow ≥ 23 with
nf-provplugin (configured automatically bysfprov init)
1 maintainer
Metadata
1 maintainer
Release files for sfprov 0.1.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| sfprov-0.1.2.tar.gz | 100.2 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| sfprov-0.1.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 195.9 kB
Release files / sfprov-0.1.2.tar.gz
| Download URL | sfprov-0.1.2.tar.gz |
|---|---|
| Size | 100.2 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
2160ae61972641ac8e8979d1ee3553b5b6116fcf11a2bed15c991101ba39405e
|
|
BLAKE2b-256 checksum How to use checksums |
a9b1c063b4e88e7d41eebf4b5327fdccf0c5a40fdcfd153880a21c385ef63963
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.10.15
|
Release files / sfprov-0.1.2-py3-none-any.whl
| Download URL | sfprov-0.1.2-py3-none-any.whl |
|---|---|
| Size | 95.6 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
3d65456988b97da7659906abfffdb951f3b912c91d4fc4f117a8fd584a46b108
|
|
BLAKE2b-256 checksum How to use checksums |
882ad718d52e532e482a70aa2752b667fb817a53e98270f3461c03d36a3e583b
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.10.15
|
