Changelog

Version 7.18.0-6.9.0 (2026-05-13)

Features

  • BaseSpace auto-import now supports v3 sample sheets, plus a new --run-match, --run-experiment-match option to filter which BaseSpace runs are imported. v3 sample sheets require a ProjectName column; this enables per-pool project filtering during BaseSpace auto-import.

Fixes

  • Multi-run Capture ID uploads resume logic was fixed and now resume correctly
  • export command now retries correctly on transient failures
  • IAM client is now closed properly
  • CLI now shuts down correctly in all cases while preserving non-zero exit codes

Version 7.17.0-6.8.0 (2026-04-14)

Features

  • New specimen_id column in the sample sheet CSV, propagated through analysis definitions and run creation.
  • new command can now update an existing order in addition to creating one, and accepts new diseaseIds on orders. Order IDs in the sample sheet are validated up-front before any upload starts.

Fixes

  • Sample groups are no longer formed across paired samples (e.g. Tumor/Normal or DNA/RNA pairs) that target different pipelines — pairs with mismatched pipeline IDs are now uploaded as independent samples instead of being incorrectly grouped.
  • Upload retry logic updated: upload read timeout was fixed (set to 5 minutes). Also explicit write timeout has been added.
  • status --pipeline-info now raises a clear No Run found with the query RunRef … and sampleID … error when no NGS run matches, matching the behaviour of the other status subcommands.

Version 7.16.0-6.7.0 (2026-04-01)

Features

  • Files are now uploaded sequentially per sample group (e.g. Tumor/Normal or DNA/RNA pairs). All files belonging to one group are fully uploaded before starting the next.
  • New --dry-run flag on the new command: validates the sample sheet and shows planned actions without making any changes.
  • New order_type column in sample sheet CSV (accepted values: GEN1 or GEN2).
  • sample command returns enriched data (pipeline, kit, sequencer, gene panel) when platform services are activated.

Fixes

  • Resume upload no longer recalculates MD5 for files already fully uploaded on the server.
  • IAM HTTP 401 now prompts the user to re-login; other HTTP errors show a temporary-failure message. Session token is preserved in both cases.