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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 bump many docker versions, patching CVE-2026-45447 by @dpark01 in https://github.com/broadinstitute/viral-pipelines/pull/660 Full Changelog: https://github.com/broadinstitute/viral-pipelines/compare/v3.0.15.0...v3.0.16.0
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 viral-ngs and py3-bio dockers by @dpark01 in https://github.com/broadinstitute/viral-pipelines/pull/657 Quote WDL File variable expansions to handle paths with spaces by @dpark01 in https://github.com/broadinstitute/viral-pipelines/pull/658 Sanitize Terra table names to prevent upload failures by @dpark01 in https://github.com/broadinstitute/viral-pipelines/pull/659 Full Changelog: https://github.com/broadinstitute/viral-pipelines/compare/v3.0.13.0...v3.0.15.0
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 docker images by @dpark01 in https://github.com/broadinstitute/viral-pipelines/pull/656 Full Changelog: https://github.com/broadinstitute/viral-pipelines/compare/v3.0.11.0...v3.0.13.0
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 viral-ngs to 3.0.9 by @dpark01 in https://github.com/broadinstitute/viral-pipelines/pull/649 bump viral-ngs 3.0.10, remove GATK IndelRealigner deps, update lofreq pipeline by @dpark01 in https://github.com/broadinstitute/viral-pipelines/pull/650 fix tar_extract: switch LOCAL to HDD disk, bump cpu and preemptible by @dpark01 in https://github.com/broadinstitute/viral-pipelines/pull/651 Bump docker image …
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 modular agent skills framework by @dpark01 in https://github.com/broadinstitute/viral-ngs/pull/1054 Fix tag cleanup to prevent cascade deletion of shared-digest images by @dpark01 in https://github.com/broadinstitute/viral-ngs/pull/1055 Bump pyopenssl conda pin to >=26.0.0 by @dpark01 in https://github.com/broadinstitute/viral-ngs/pull/1056 Enforce Trivy severity filter on SARIF output …
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 container vulnerability scanning with Trivy by @dpark01 in https://github.com/broadinstitute/viral-ngs/pull/1052 Replace GATK with FreeBayes for variant calling; upgrade Java tools to eliminate CVEs by @dpark01 in https://github.com/broadinstitute/viral-ngs/pull/1053 Full Changelog: https://github.com/broadinstitute/viral-ngs/compare/v3.0.9...v3.0.10
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 py3-bio from 0.1.3 to 0.1.4 by @dpark01 in https://github.com/broadinstitute/viral-pipelines/pull/646 fix: update illumina import for viral-ngs 3.x namespace restructure by @dpark01 in https://github.com/broadinstitute/viral-pipelines/pull/647 bump viral-ngs and nextclade docker images by @dpark01 in https://github.com/broadinstitute/viral-pipelines/pull/648 Full Changelog: https://github.com/broadinstitute/viral-pipelines/compare/v3.0.7.0...v3.0.8.0
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 Fix outer barcode matching: consensus, fuzzy matching, samplesheet-authoritative metrics by @dpark01 in https://github.com/broadinstitute/viral-ngs/pull/1048 Full Changelog: https://github.com/broadinstitute/viral-ngs/compare/v3.0.7...v3.0.8
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 arm64 cryptography ImportError by pip-installing firecloud by @dpark01 in https://github.com/broadinstitute/viral-ngs/pull/1044 Remove conda/mamba symlinks that cause micromamba subprocess warnings by @dpark01 in https://github.com/broadinstitute/viral-ngs/pull/1043 Fix --version returning timestamp when CWD lacks VERSION file by @dpark01 in https://github.com/broadinstitute/viral-ngs/pull/1045 Switch Docker builds to …
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 bugfix: task terra.create_or_update_sample_tables by @dpark01 in https://github.com/broadinstitute/viral-pipelines/pull/640 Remove maxRetries to restore Cromwell call caching by @dpark01 in https://github.com/broadinstitute/viral-pipelines/pull/641 bump viral-ngs 3.0.6 to 3.0.7 by @dpark01 in https://github.com/broadinstitute/viral-pipelines/pull/644 move all viral-ngs WDL tasks back to quay.io from ghcr.io by @dpark01 in …
us, ru, jp, de, gb (code pays fourni par la source)
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