FastaGuard v0.6.0

FastaGuard v0.6.0

Workflow-Compatible Exit Contract

FastaGuard now separates command execution from FASTA quality decisions.
Successful report generation exits with code 0, including reports whose
verdict or gate status is WARN or FAIL. Argument parsing errors exit with
code 2, while configuration, input-access, and runtime errors exit with code
3.

QC decisions remain explicit in the report contract:

• verdict.status records the overall PASS/WARN/FAIL result.
• gate.status records the selected gate result.
• gate.blocking_findings lists findings that should stop downstream work.
• single-file TSV reports include input_path, verdict, and gate_status.
• compare TSV reports retain one row per input with its path and status fields.

This keeps JSON and TSV reports available to Nextflow, Snakemake, nf-core, and
other workflow engines. Pipelines can publish the evidence first and apply
their own stop/go policy downstream.

Migration

Workflows that previously interpreted process exit codes 1 and 2 as WARN
and FAIL should instead read gate.status or verdict.status from JSON or TSV.
The repository includes examples/workflows/check_fastaguard_gate.py for
workflows that need a separate enforcement step after reports are collected.

The JSON schema and finding catalog remain at version 0.5.0 because their
structures and finding semantics are unchanged in this release.