FastaGuard v0.3.0

FastaGuard v0.3.0

FastaGuard v0.3.0 is the Evidence And Assembly Gate release.

This release makes FastaGuard more useful as an early, machine-readable
assembly preflight gate before QUAST, BUSCO, BlobToolKit, CheckM, annotation,
or other expensive downstream QC.

Highlights

• Adds --gate pipeline, a conservative assembly gate preset for pipeline
  automation.
• Adds a machine-readable gate report object with mode, status, blocking
  findings, advisory findings, and the active failure policy.
• Adds provenance.input_sha256 so workflow engines and agents can tie a
  report back to the exact FASTA bytes that were checked.
• Updates JSON, TSV, HTML, and MultiQC-compatible outputs with the v0.3 report
  contract.
• Keeps stable finding IDs and structured actions as the source of truth for
  automation.
• Supports the v0.3 evidence workflow without requiring databases or external
  services for normal runs.

Install

Download the platform binary from this GitHub release, or build from source:

cargo install --git https://github.com/ehsanestaji/FastaGuard --tag v0.3.0
fastaguard --version

Bioconda and BioContainers updates should follow after the v0.3.0 source
archive and release assets are public.

Pipeline Gate

Use the assembly gate when FastaGuard should make a pipeline decision:

fastaguard sample.fa --gate pipeline \
  --out fastaguard_report.html \
  --json fastaguard.json \
  --tsv fastaguard.tsv \
  --multiqc fastaguard_mqc.json

--gate pipeline fails on conservative FASTA-level blockers such as invalid
FASTA structure, invalid characters, duplicate identifiers, and high global N
rate. Other findings can still be emitted as advisory evidence, so downstream
workflow logic can distinguish "stop and fix the FASTA" from "continue, but
route to deeper assembly QC."

Machine-Readable Outputs

The JSON report remains the source of truth. The v0.3.0 contract adds:

• gate.mode and gate.status for direct pipeline decisions.
• gate.blocking_findings and gate.advisory_findings for routing.
• gate.fail_on for the active failure policy after preset expansion.
• provenance.input_sha256 for input identity checks.
• Pipeline-friendly TSV fields that surface gate status and input checksum
  alongside the usual summary metrics.
• MultiQC-compatible fields that surface gate mode, gate status, and blocking
  finding IDs alongside the usual summary metrics.

Evidence Workflow

The evidence workflow for v0.3.0 is intended to show that the assembly gate,
report schema, provenance checksum, and committed examples are reproducible.
The workflow should use local FASTA metrics only; FastaGuard does not fetch
taxonomy databases or make biological completeness claims.

Known Limits

• FastaGuard remains a FASTA preflight tool, not a replacement for QUAST,
  BUSCO, BlobToolKit, CheckM, seqkit, MultiQC, or annotation workflows.
• --gate pipeline is intentionally conservative and database-free.
• Composition and outlier findings are triage signals, not contamination or
  taxonomic assignments.
• input_sha256 identifies the checked input bytes; it does not by itself
  prove sample identity, biological quality, or reference correctness.