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fix: use conventional exit codes for reports#18

Merged
ehsanestaji merged 2 commits into
mainfrom
fix/conventional-exit-codes
Jul 16, 2026
Merged

fix: use conventional exit codes for reports#18
ehsanestaji merged 2 commits into
mainfrom
fix/conventional-exit-codes

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@ehsanestaji

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Summary

  • return process exit 0 whenever FastaGuard successfully writes requested reports, regardless of PASS/WARN/FAIL QC status
  • keep QC decisions in report fields such as verdict.status, gate.status, and gate.blocking_findings
  • simplify local Snakemake and nf-core starter examples by removing captured exit-code workarounds

Why

This aligns FastaGuard with standard CLI/workflow expectations raised during Snakemake and nf-core wrapper review: process exit should indicate tool execution success/failure, while QC gating should be handled from machine-readable report fields.

Verification

  • cargo fmt --all --check
  • cargo test --locked --all-targets
  • cargo clippy --locked --all-targets -- -D warnings
  • python3 -m unittest discover -s tests/python

Follow-up after merge/release

  • publish a patch release before updating external workflow PRs
  • simplify the Snakemake wrapper PR
  • simplify the nf-core module PR

Bump the package version, add input paths to single-file TSV reports, preserve compatibility for pinned v0.5 wrappers, and document the migration to report-based QC routing.
@ehsanestaji
ehsanestaji marked this pull request as ready for review July 16, 2026 20:23
@ehsanestaji
ehsanestaji merged commit cf27295 into main Jul 16, 2026
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