Merge pull request #31 from dholab/v3.3.0-rc

v3.3.0 release candidate

Merge pull request #44 from dholab/v3.2.1-rc

v3.2.1 release candidate

fix: update test to match new None value replacement

test: cover the LabKey hits list reference cutoff

Exercise apply_reference_cutoff: a top-bitscore tie larger than the retention count is bounded to K references and truncated deterministically to the lowest sseqids, and the cutoff is scoped per (sample_id, qseqid) so a multi-taxid reference counts as a single hit with all of its rows retained.

ci: upload integration diagnostics on failure

Add a narrow failure-only artifact upload to the mini SRA integration workflow. The bundle keeps the files most useful for diagnosing disappearing samples: Nextflow logs, the latest e2e pointer, captured stdout/stderr, the Nextflow report, final per-sample BLAST TSVs, experiment-summary TSVs, and per-task command logs plus exit codes.

The artifact intentionally avoids broad work-directory uploads so downloaded FASTQs and larger bioinformatics intermediates do not get retained. Retention is set to the GitHub Actions minimum of one day, which is the closest supported value to a short-lived debugging window.

final repo text polish and small fixes for release

fix: add repair_pairs to params schema

The validate_schema_completeness CI check failed because repair_pairs
was added to nextflow.config but not to the JSON schema.

Merge pull request #18 from dholab/v2.5.1-rc

v2.5.1: fix channel gating bugs and CLI -resume misparse

v2.5.0 release candidate

making sure main.nf and nextflow.config are present in the containerfile