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