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Daniel Park, Chris Tomkins-Tinch, Simon Ye, Irwin Jungreis et autres
What's Changed Fix assembly-metadata TSV column order: stop relying on keys() ordering by @dpark01 in https://github.com/broadinstitute/viral-pipelines/pull/683 Full Changelog: https://github.com/broadinstitute/viral-pipelines/compare/v3.0.24.0...v3.0.24.1
us, ru, jp, de, gb (code pays fourni par la source)
Daniel Park, Chris Tomkins-Tinch, Simon Ye, Irwin Jungreis et autres
What's Changed find_illumina_files: find fastqs in nested run folders, and stop failing silently by @dpark01 in https://github.com/broadinstitute/viral-pipelines/pull/680 bump viral-ngs 3.0.22, and cover no-lane-splitting FASTQ names in CI by @dpark01 in https://github.com/broadinstitute/viral-pipelines/pull/681 bump viral-ngs 3.0.24, and cover single-sample 3-barcode pools in CI by …
us, ru, jp, de, gb (code pays fourni par la source)
Daniel Park, Chris Tomkins-Tinch, Simon Ye, Irwin Jungreis et autres
What's Changed Identify a pool by its barcodes in splitcode_demux by @dpark01 in https://github.com/broadinstitute/viral-ngs/pull/1118 Full Changelog: https://github.com/broadinstitute/viral-ngs/compare/v3.0.23...v3.0.24
us, ru, jp, de, gb (code pays fourni par la source)
Daniel Park, Chris Tomkins-Tinch, Simon Ye, Irwin Jungreis et autres
What's Changed Accept DRAGEN FASTQ names with no lane token (#1113) by @dpark01 in https://github.com/broadinstitute/viral-ngs/pull/1114 Full Changelog: https://github.com/broadinstitute/viral-ngs/compare/v3.0.21...v3.0.22
us, ru, jp, de, gb (code pays fourni par la source)
Daniel Park, Chris Tomkins-Tinch, Simon Ye, Irwin Jungreis et autres
What's Changed Fix two wrong assumptions about 3-barcode pool shape (#1115) by @dpark01 in https://github.com/broadinstitute/viral-ngs/pull/1116 Full Changelog: https://github.com/broadinstitute/viral-ngs/compare/v3.0.22...v3.0.23
us, ru, jp, de, gb (code pays fourni par la source)
Daniel Park, Chris Tomkins-Tinch, Simon Ye, Irwin Jungreis et autres
What's Changed Retire M-Vicuna deduplication from the remaining workflows by @dpark01 in https://github.com/broadinstitute/viral-pipelines/pull/674 Bump VADR docker 1.6.4 -> 1.7; fetch SARS-CoV-2 models explicitly by @dpark01 in https://github.com/broadinstitute/viral-pipelines/pull/675 Fix nextclade_many_samples reading tag.json instead of pathogen.json by @dpark01 in https://github.com/broadinstitute/viral-pipelines/pull/673 bump docker image versions: …
us, ru, jp, de, gb (code pays fourni par la source)
Daniel Park, Chris Tomkins-Tinch, Simon Ye, Irwin Jungreis et autres
What's Changed Add clumpify-based dedup and drop the M-Vicuna dependency by @dpark01 in https://github.com/broadinstitute/viral-ngs/pull/1112 Full Changelog: https://github.com/broadinstitute/viral-ngs/compare/v3.0.20...v3.0.21
us, ru, jp, de, gb (code pays fourni par la source)
Daniel Park, Chris Tomkins-Tinch, Simon Ye, Irwin Jungreis et autres
What's Changed Enforce the viral-pipelines samplesheet schema before demux by @dpark01 in https://github.com/broadinstitute/viral-pipelines/pull/665 Speed up DNAnexus workflow compilation by @dpark01 in https://github.com/broadinstitute/viral-pipelines/pull/666 bump viral-ngs 3.0.19 -> 3.0.20 by @dpark01 in https://github.com/broadinstitute/viral-pipelines/pull/667 Rename requirements-modules.txt to docker-versions.txt; fix stale AGENTS.md reference by @dpark01 in …
us, ru, jp, de, gb (code pays fourni par la source)
Daniel Park, Chris Tomkins-Tinch, Simon Ye, Irwin Jungreis et autres
What's Changed Unblock the CVE auto-fix bot: verify conda availability before triage by @dpark01 in https://github.com/broadinstitute/viral-ngs/pull/1108 Add .trivyignore entry for CVE-2025-47273 (phantom setuptools from pip's vendored SBOM) by @dpark01 in https://github.com/broadinstitute/viral-ngs/pull/1110 Auto-fix: address open CVE issues (2026-08-04) by @viral-ngs-autofix[bot] in https://github.com/broadinstitute/viral-ngs/pull/1109 Full …
us, ru, jp, de, gb (code pays fourni par la source)
Daniel Park, Chris Tomkins-Tinch, Simon Ye, Irwin Jungreis et autres
What's Changed bump docker images (CVE patch releases): viral-ngs 3.0.19, py3-bio 0.1.12, read-qc-tools 1.1.3 by @dpark01 in https://github.com/broadinstitute/viral-pipelines/pull/664 Full Changelog: https://github.com/broadinstitute/viral-pipelines/compare/v3.0.17.1...v3.0.19.0
us, ru, jp, de, gb (code pays fourni par la source)
Daniel Park, Chris Tomkins-Tinch, Simon Ye, Irwin Jungreis et autres
What's Changed Bump CVE-triage CI from Claude Sonnet 4.6 to Sonnet 5 by @dpark01 in https://github.com/broadinstitute/viral-ngs/pull/1100 ci: fix CVE-triage Sonnet 5 compat, bump build-push-action to Node 24, pin Trivy to v0.72.0 by @dpark01 in https://github.com/broadinstitute/viral-ngs/pull/1102 Bump Pillow to 12.3.0 for CVE fixes …
us, ru, jp, de, gb (code pays fourni par la source)
Daniel Park, Chris Tomkins-Tinch, Simon Ye, Irwin Jungreis et autres
What's Changed Pin rpds-py 2026.6.3 to fix PyO3 vulnerability by @dpark01 in https://github.com/broadinstitute/viral-ngs/pull/1106 Full Changelog: https://github.com/broadinstitute/viral-ngs/compare/v3.0.18...v3.0.19
us, ru, jp, de, gb (code pays fourni par la source)
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