chore(release): release main

[MVHBot]

grz-tools release (2026-05-11)

This release updates multiple packages in the grz-tools monorepo. See the full changelog and per-package details linked below.

Versions

• grzctl 2.0.0 (from 1.4.0)
• grz-db 2.0.0 (from 1.2.0)
• grz-common 2.0.0 (from 1.6.1)
• grz-cli 1.6.0 (from 1.5.1)
• grz-pydantic-models 2.6.0 (from 2.5.0)
• grz-check 0.3.0 (from 0.2.1)

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⚠️ Breaking / behavior changes

• grzctl now automatically updates submission state in the DB on subcommand invocation (default --update-db; use --no-update-db to disable). The DB state enum adds REPORTING. (feat(grzctl)!: Automatically update submission state upon subcommand invocation #501)
• grzctl pruefbericht submit now requires --submission-id so the submission can be updated consistently in the DB. (feat(grzctl): implement Prüfbericht generation using submission ID from database #525)
• grz-cli enforces a version policy via S3 version.json for upload / submit operations. (feat(grz-cli,grz-common): Add version checks to upload/submit #477)
• Added selected_for_qc column and QC workflow version recording; tools now require/record QC workflow version and log grzctl runtime version. (feat(grz-db,grzctl): add selected_for_qc submission column to submission database #531, feat(grz-cli, grz-db): require & record QC workflow version; log grzctl runtime version (closes #532) #561)
• grzctl db submission populate-qc now requires --qc-workflow-version (or GRZCTL_QC_WORKFLOW_VERSION) to be provided so the QC workflow version can be recorded in the DB. (feat(grz-cli, grz-db): require & record QC workflow version; log grzctl runtime version (closes #532) #561)
• grzctl introduces backfill to re-read metadata from archives and other state/reporting improvements (impacting automation that reads/writes the submission DB). (feat(grzctl): Introduce "backfill" command to re-read metadata from the archive #559)
• Dropped the Python dependency pysam from grz-cli, grzctl, and grz-common (installs are lighter; environments that relied on it being installed transitively must install it explicitly). (chore(grz-cli,grz-common,grzctl): drop pysam dependency #565)

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Highlights

grz-cli (1.6.0)

• Version policy checks for upload and submit via S3 version.json (feat(grz-cli,grz-common): Add version checks to upload/submit #477)
• Multiple config files are merged into one effective configuration (feat(grzctl,grz-cli,grz-common): Merge multiple configuration files #490)
• upload now prints the generated submission ID to stdout (can affect scripts that parse command output). (fix(grz-cli): Submission id upload tracking #556)

grzctl (2.0.0)

• db list: state-based filtering, with “latest” view by default (feat(grzctl): add state-based filtering to grzctl db list (latest by default) #523)
• db submission show: --json output (feat(grzctl): Add --json output to grzctl db submission show #510)
• Prüfbericht generation using submission ID from database (feat(grzctl): implement Prüfbericht generation using submission ID from database #525)
• report: makes identifiers.le optional (feat(grzctl): Make 'identifiers.le' config optional for 'grzctl report' command #488)
• report supports --with-submission-ids. (feat(grzctl): submission-id for grzctl report with option --with-submission-ids #539)
• Improved redaction during archival. (feat(grzctl): Improved redaction during archival #517)
• Add selected_for_qc column to the submission database (feat(grz-db,grzctl): add selected_for_qc submission column to submission database #531)
• populate-qc: accept THRESHOLD NOT MET as valid QC status (fix(grzctl): accept THRESHOLD NOT MET as valid QC status in populate-qc #529)
• Fix displayed QC stats (fix(grzctl): fix displayed QC stats #508)
• Introduce backfill to re-read metadata from the archive (feat(grzctl): Introduce "backfill" command to re-read metadata from the archive #559)
• Require and record QC workflow version; log grzctl runtime versions (feat(grz-cli, grz-db): require & record QC workflow version; log grzctl runtime version (closes #532) #561)
• db tui: add --quarter/--year selection for the “Detailed QC by LE” overview. (grzctl db tui: add --quarter/--year selection for “Detailed QC by LE” overview (closes #502) #541)

grz-pydantic-models (2.6.0)

• Enforce differing checksums for sequencing data (feat(grz-pydantic-models): Enforce differring checksums for sequencing data #496)
• Fix MII consent period to use datetime instead of date (fix(grz-pydantic-models,grz-cli,grzctl): Fix MII Consent Period to use datetime instead of date #491)
• Change minReadLength default from 0 to -1 (fix(grz-pydantic-models): Change minReadLength default from 0 to -1 #506)

grz-check (0.3.0)

• Python bindings now power checksum validation across the stack (feat(grz-cli,grzctl,grz-common,grz-check): use grz check python bindings #554)
• Checksum calculation is now exposed correctly in the Python API (#5dce167)
• grz-check is now built and published as a Python package via pyproject.toml/maturin. (feat(repo, grz-check) V2: Build and publish grz-check as pyproject as well #543)

Maintenance

• Dependency updates (fix(repo): Update dependencies #498)
• Python crypto dependency updates: pynacl and crypt4gh

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Rollout notes (ops)

• Apply the submission DB migrations before using this release. The schema changes include selected_for_qc, QC workflow version logging, grzctl runtime version logging, and the new REPORTING state.
• Submission DB migrations in this release also include the qc_queue table and additional submissions fields (submission_size, submission_metadata)—make sure your DB is migrated to head before running the updated tools.
• Update any automation that calls grzctl pruefbericht submit to pass --submission-id.
• If you enforce LE uploads via S3, deploy the version.json policy for grz-cli.
• Deploy the matching grz-check Python bindings where Python-based checksum validation is used.

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Full details

• Full changelog: changes.md
• Per-package changelogs:
  • packages/grz-cli/CHANGELOG.md
  • packages/grzctl/CHANGELOG.md
  • packages/grz-common/CHANGELOG.md
  • packages/grz-db/CHANGELOG.md
  • packages/grz-pydantic-models/CHANGELOG.md
  • packages/grz-check/CHANGELOG.md