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FastaGuard v1.0.0 — Reference Contract Gate
Release
FastaGuard v1.0.0 introduces the Reference Contract Gate while preserving the
established assembly, compare, report, and workflow interfaces.
Reference compatibility
fastaguard reference compares explicitly supplied reference declarations with
one canonical FASTA. It supports FAI files, SAM sequence dictionaries, BAM and
CRAM headers, VCF and BCF contig declarations, and GFF3 sequence declarations.
It does not discover sidecar files implicitly or inspect alignment and variant
records.
The command provides strict, coordinate, and advisory policies; reports stable
findings in JSON, TSV, HTML, and MultiQC-compatible outputs; and can write a
portable lockfile for the reference identity and declared artefacts.
Report contract
Assembly reports retain schema version 0.7.0 and now include the additive
report_type: "assembly" discriminator. Compare reports retain
report_type: "compare" and schema version 0.7.0. Reference reports use
report_type: "reference" and Reference Contract schema version 1.0.0.
The nf-core and Snakemake integrations keep their existing workflow interfaces.
Measured workflow value
On a 4.42-million-pair E. coli dataset, FastaGuard detected a one-base
reference-index mismatch before mapping, avoiding a 45-second mapping-and-
sorting task in both Snakemake and Nextflow. The measurement is scoped to the
documented controlled baseline and does not claim a universal saving. See the
workflow savings benchmark for the method
and results.
Downstream availability
The GitHub release includes the executable, README, licence, JSON Schema,
finding catalogue, and SHA-256 checksums. Bioconda and BioContainers remain at
v0.7.0 until the downstream recipe update is merged and published. The existing
nf-core module and Snakemake wrapper continue to use that published package in
the meantime.
The release is validated with deterministic Rust and Python tests, schema and
archive checks, and local workflow smoke tests.