v3.0.17.1

What's Changed

• WDL 1.1 language modernization: keys()/as_pairs()/as_map() by @dpark01 in #662
• Wire inner-barcode trim knobs into demux_fastqs by @dpark01 in #663

Full Changelog: v3.0.17.0...v3.0.17.1

v3.0.17.0

What's Changed

• bump viral-ngs and py3-bio dockers by @dpark01 in #661
• Upgrade WDL from 1.0 to 1.1 by @dpark01 in #635

Full Changelog: v3.0.16.0...v3.0.17.0

v3.0.16.0

What's Changed

• bump many docker versions, patching CVE-2026-45447 by @dpark01 in #660

Full Changelog: v3.0.15.0...v3.0.16.0

v3.0.15.0

What's Changed

• bump viral-ngs and py3-bio dockers by @dpark01 in #657
• Quote WDL File variable expansions to handle paths with spaces by @dpark01 in #658
• Sanitize Terra table names to prevent upload failures by @dpark01 in #659

Full Changelog: v3.0.13.0...v3.0.15.0

v3.0.13.0

What's Changed

• bump docker images by @dpark01 in #656

Full Changelog: v3.0.11.0...v3.0.13.0

v3.0.11.0

What's Changed

• bump viral-ngs to 3.0.9 by @dpark01 in #649
• bump viral-ngs 3.0.10, remove GATK IndelRealigner deps, update lofreq pipeline by @dpark01 in #650
• fix tar_extract: switch LOCAL to HDD disk, bump cpu and preemptible by @dpark01 in #651
• Bump docker image versions for ncbi-tools, nextclade, read-qc-tools, pangolin by @dpark01 in #652
• Adjust preemptible settings for assembly/metagenomics tasks by @dpark01 in #654
• Add rasusa-based coverage downsampling and tune preemptible settings by @dpark01 in #655

Full Changelog: v3.0.8.0...v3.0.11.0

v3.0.8.0

What's Changed

• bump py3-bio from 0.1.3 to 0.1.4 by @dpark01 in #646
• fix: update illumina import for viral-ngs 3.x namespace restructure by @dpark01 in #647
• bump viral-ngs and nextclade docker images by @dpark01 in #648

Full Changelog: v3.0.7.0...v3.0.8.0

v3.0.7.0

What's Changed

• bugfix: task terra.create_or_update_sample_tables by @dpark01 in #640
• Remove maxRetries to restore Cromwell call caching by @dpark01 in #641
• bump viral-ngs 3.0.6 to 3.0.7 by @dpark01 in #644
• move all viral-ngs WDL tasks back to quay.io from ghcr.io by @dpark01 in #645

Full Changelog: v3.0.6.0...v3.0.7.0

v3.0.6.0

What's Changed

• viral-ngs 3.0.5 to 3.0.6 by @dpark01 in #639

Full Changelog: v3.0.5.0...v3.0.6.0

v3.0.5.0

What's Changed

• viral-ngs: 3.0.5 by @dpark01 in #638

Full Changelog: v3.0.4.0...v3.0.5.0