v2.1.28.0
new features:
- new workflow sarscov2_nextstrain [#204, #208, #219]
- updates to genbank submission [#201, #207]
- update vadr alert criteria based on NCBI recommendations [#234, #249]
- add nextclade tree outputs to sarscov2_illumina_full [#233]
- add sequencing reports via rmarkdown (sarscov2_illumina_full) [#222, #226, #228, #235, #236, #244, #245, #248, #265]
- ivar trim updates: emit ivar trim stats (assemble_refbased) and compute summary stats (sarscov2_illumina_full) [#237]
- terra table upload and download [#206, #241]
- add picard wgs metrics, alignment metrics, and insert size metrics to assemble_refbased and sarscov2_illumina_full [#239, #282]
- add bucket delivery of data for CDC, SRA, and GP reporting to sarscov2_illumina_full [#258, #263, #278]
- add tasks and workflows for NCBI BioSample registration and metadata retrieval [#279]
- automated filtering of libraries from failed NTC controls [#266]
bug fixes:
- bugfix whitespace handling in gzcat task [#230]
- deduplicate output rows from sra_meta_prep [#220]
- GISAID metadata output should be CSV not TSV [#273]
- derive Illumina run ID from XML instead of tarball filename [#275]
minor updates to docker images and vm shapes:
- vm shape updates on augur steps [#205, #224, #225, #229, #232]
- bump viral-core docker [#242, #243, #268, #270, #274, #276, #281, #284]
- bump ivar docker [#209]
- bump pangolin/pangolearn [#203, #205, #210, #213, #214, #215, #216, #217, #218, #240, #250, #254, #267, #271, #285]
- bump vadr docker [#216, #264]
- bump nextstrain/base [#238]
- bump sc2-rmd docker [#269, #277]
- update nextmeta tsv output behavior to match new nextmeta spellings [#231]
build changes: