v2.2.4.0

What's Changed

New workflows

• Enterics QC visualizations
  • WDL for creating Enterics Visualizations by @schaluva in #500
  • create generalized version of enterics visualization WDL by @schaluva in #501
  • Visualization HTML PR by @jpramosbarroso in #513
  • Fixing duplicate inputs bug by @jpramosbarroso in #514
  • integrating threshold file by @jpramosbarroso in #515
• Terra-on-GCP-specific features
  • add check_terra_env task by @tomkinsc in #497
  • add workflows to add to or create library and sample tables based on demultiplexing output by @tomkinsc in #507
  • mark check_terra_env task as volatile by @tomkinsc in #510
  • include user email among outputs of check_terra_env task by @tomkinsc in #508
• transmission reconstruction from @ispecht
  • add reconstructR workflow by @dpark01 in #504
• mass-scale metagenomic denovo assembly
  • add new workflow scaffold_and_refine_multitaxa by @dpark01 in #506
  • more scaffolding updates by @dpark01 in #511

Updates to existing workflows

• pass through sbt template if optional defaults_yaml is not provided and author_list string is empty by @tomkinsc in #492
• mark downsample_bams task as volatile (nondeterministic) by @tomkinsc in #494
• expose numberOfNegativeControls in illumina_demux by @tomkinsc in #498
• add masked_positions and masked_positions_file arguments to task polyphonia_detect_cross_contamination by @lakras in #499
• fix mem high watermark reporting by @tomkinsc in #502
• mass update of upstream docker tags by @dpark01 in #505
  • broadinstitute/viral-core: 2.1.33 -> 2.2.4
  • broadinstitute/viral-classify: 2.1.33.0 -> 2.2.3.0 (later bumped to 2.2.4.0 in #511)
  • broadinstitute/viral-baseimage: 0.1.20 -> 0.2.0
  • staphb/vadr: 1.5.1 -> 1.6.3
  • staphb/pangolin: 4.3.1-pdata-1.22 -> 4.3.1-pdata-1.23.1
  • nextstrain/nextclade: 2.12.0 -> 2.14.0

Build and CI

• enable merge_group builds in github actions CI by @dpark01 in #503
• allow docker image pinning to be skipped with #skip-global-version-pin annotation by @tomkinsc in #493
• dockstore updates by @dpark01 in #512
• clean up disk space in Github Actions VMs #505

New Contributors

• @jpramosbarroso made their first contribution in #513
• @ispecht 's code is utilized in a new workflow for #504

Full Changelog: v2.1.33.17...v2.2.4.0