v2.1.33.9

This release fixes a consistent major failure mode (which only emerged recently) when executing most assembly, demux, or phylogenetic workflows on Google Cloud (e.g., via Terra).

What's Changed

• make memory telemetry fail gracefully by @dpark01 in #413

Full Changelog: v2.1.33.8...v2.1.33.9

v2.1.33.8

See release notes for v2.1.33.7, which failed to sync to Dockstore. v2.1.33.8 has no non-whitespace changes from v2.1.33.7, and is only meant to fix the sync.

Full Changelog: v2.1.33.6...v2.1.33.8

v2.1.33.7

What's Changed

• sc2 sequencing report ram and pangolin update fault tolerance by @dpark01 in #410
• pangolin v4 by @dpark01 in #411

Full Changelog: v2.1.33.6...v2.1.33.7

v2.1.33.6

What's Changed

• update pangolin and nextclade docker images by @dpark01 in #409

Full Changelog: v2.1.33.5...v2.1.33.6

v2.1.33.5

What's Changed

• post CDC contract: genome ID renaming by @dpark01 in #408

Full Changelog: v2.1.33.4...v2.1.33.5

v2.1.33.4

What's Changed

• increase tsv_join default mem 7->15 GB by @tomkinsc in #406
• update pangolin container by @dpark01 in #407

Full Changelog: v2.1.33.3...v2.1.33.4

v2.1.33.3

What's Changed

docker image updates

• nextclade 1.7.0 to 1.10.0 by @dpark01 in #404
• pangolin container update by @dpark01 in #405

Full Changelog: v2.1.33.2...v2.1.33.3

v2.1.33.2

What's Changed

new features / behavior

• new read_depths workflow by @lakras in #393
• tsv_join task: add option to control preference of input order (left or right join) by @dpark01 in #400

optimizations / vm tuning

• parameterize memory for tasks_nextstrain.tip_frequencies task; increase default to 30GB by @tomkinsc in #398

docker image updates

• bump panoglin 3.1.16 -> 3.1.17 and nextclade 1.4.0 -> 1.7.0 by @dpark01 in #399
• update pangoLEARN, pango-designation, scorpio, constellations by @dpark01 in #401
• update vadr 1.3 -> 1.4 by @dpark01 in #402
• update pangoLEARN, pango-designation, constellations; update vadr 1.4 -> 1.4.1 by @dpark01 in #403

Full Changelog

v2.1.33.1...v2.1.33.2

v2.1.33.1

What's Changed

new features

• robustness: allow one retry for gisaid uploader [#395]

optimizations

• slight speed optimizations to assemble_refbased and demux_deplete [#397]

vm/image updates

• bump pangolearn docker [#394]
• bump vadr docker (new models for sc2) [#396]

contributors

@dpark01

Full Changelog: v2.1.33.0...v2.1.33.1

v2.1.33.0

What's Changed

new features

• turn on allowNestedInputs for subworkflows: this exposes to the end-user all task-level optional inputs from subworkflows [#387]
• expose --print-all-iSNVs option for cross-contamination detection [#386]
• add update_dbs_now option to pangolin tasks [#392]
• add generic upload_entities_tsv task [#391]
• Filter CRSP samples -> biosample registration to only clinical tests (not pooled samples) [#374]
• CRSP meta ETL: add new body part value [#390]
• add sample ID list to outputs of nextclade/pangolin many sample tasks [#373]

bug fixes

• use WDL value for submitting_lab_name in gisaid_meta_prep python body [#376]

optimizations

• allow maxRetries=2 for most WDL tasks, increasing robustness of execution on Terra [#379, #383]
• sarscov2_batch_relineage: speed up localization of input data [#375]
• descatter CDC AWS delivery: copy all raw reads in a single aws S3 copy task instead of hundreds--faster, more reliable, etc [#389]

vm/image updates

• bump viral-core image and remove in-WDL workaround [#377]
• update pangolin docker [#380, #385, #388]
• update nextstrain docker to most recent tag (20211012 ) and update ncov commit to v9 release [#378]
• increase mem of utils.tsv_join task 7GB->15GB, allow maxRetries=2 [#379]
• increase default memory for tsv_join 7->32gb [#382]
• more ram and disk for sc2 reports [#384]
• VM tuning of nextclade & pangolin many-sample tasks based on measured usage of a typical 768-sample flowcell [#373]

build updates

• github actions updates [#381]
• dnanexus build fixes [#372]

Contributors

@dpark01 @tomkinsc @lakras

Full Changelog: v2.1.32.4...v2.1.33.0