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
- transmission reconstruction from @ispecht
- mass-scale metagenomic denovo assembly
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