Releases: broadinstitute/viral-pipelines
Releases · broadinstitute/viral-pipelines
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
v2.1.33.17
What's Changed
new features or functionality
- extend beast task and workflow to glob and output *.ops, *.rates, and *.root files by @tomkinsc in #478
- Subsampler and augur workflow by @dpark01 in #483
bug fixes and small changes
- syntax bugfixes by @dpark01 in #462
- tweaks to demux_only and demux_metag by @dpark01 in #464
- omit --dirs from the MultiQC invocation to only show sample names in report by @tomkinsc in #467
- hotfix for bug in output path by @dpark01 in #480
- sc2 nextstrain: reduce temp file sizes by @dpark01 in #484
- Fetch_SRA_to_BAM - tolerate no isolate defined by @dpark01 in #489
- Update genbank.WDL so author_list input is optional by @tomkinsc in #473
documentation updates
- Enhancing documentation for viral-pipelines by @golu099 in #461
- move transposed parameter_meta block outside command block scope to where it belongs by @tomkinsc in #477
- Update LICENSE copyright year by @tomkinsc in #476
parameterization and default VM shapes
- de novo assembly & scaffold mem default 31 -> 63 GB by @tomkinsc in #465
- parameterize disk size for illumina_demux task by @tomkinsc in #470
- max_records_in_ram param 2000000 -> 10000000 for Nova S2 by @tomkinsc in #468
upstream docker tags / version dependencies
build updates and fixes
- delete the .travis directory by @tomkinsc in #448
- dnanexus CI build fixes by @dpark01 in #485 #486 #487 #488
- GitHub actions update by @tomkinsc in #474
Full Changelog: v2.1.33.16...v2.1.33.17
v2.1.33.16
What's Changed
functionality changes and bug fixes
- Convert amplicon16S_analysis workflow (QIIME) from single-sample to multi-sample by @golu099 in #452
- samtools ampliconstats needs bed in certain order by @dpark01 in #454
parameterization and defaults
- parameterize and update defaults for VM shapes in nextstrain tasks by @dpark01 in #455
- parameterize more assembly knobs by @dpark01 in #457
update docker tags / version dependencies
- update to pangolin 4.2 / pdata 1.18 by @dpark01 in #451
- Update pangolin, nextclade, and vadr docker images by @dpark01 in #456
build updates and fixes
- documentation build fixes for ReadTheDocs by @tomkinsc in #450
- update comment about DX_API_TOKEN by @tomkinsc in #449
Full Changelog: v2.1.33.15...v2.1.33.16
v2.1.33.15
What's Changed
new and changed workflows
- Add workflow for QIIME2 classification of 16S reads by @golu099 in #439
- simplify augur_from_assemblies workflow by @dpark01 in #440
- denovo assembly SPAdes updates by @dpark01 in #441
- genbank prep and assemble_denovo updates by @dpark01 in #443
- add new workflow nextclade_single by @dpark01 in #444
- update classify_single to accept multiple bams by @dpark01 in #447
smaller docker, VM, and mechanical updates
- more disk for nextstrain; dockstore API fix by @dpark01 in #437
- Make Pipelines Azure compatible Closes #143 by @vsmalladi in #438
- set default GPU to K80->P4 in BEAST task; parameterize beagle_order by @tomkinsc in #442
- pangolin 4.1.3 / pdata 1.17 by @dpark01 in #445
New Contributors
- @vsmalladi made their first contribution in #438
- @golu099 made their first contribution in #439
Full Changelog: v2.1.33.14...v2.1.33.15
v2.1.33.14
What's Changed
Feature changes
Docker image updates
- update nextclade and vadr docker images by @dpark01 in #433
- bump pangolin to 4.1.2-1.14 and nextclade to 2.5.0 by @dpark01 in #434
Full Changelog: v2.1.33.13...v2.1.33.14
v2.1.33.13
What's Changed
Feature changes
- CDC SC2 viral pipeline updates (parameters, reporting, QC) by @dpark01 in #431
- expose exclude/drop list input for nextstrain_build_subsample task by @tomkinsc in #428
Docker image updates
- nextclade 2.0 updates by @dpark01 in #430
- update pangolin docker to 4.1.1-pdata-1.11 by @dpark01 in #432
VM shape tuning
- parameterize machine_mem_gb for ancestral_traits task by @tomkinsc in #427
- in export_auspice_json parameterize task mem, raise default to 64GB; increase AUGUR_RECURSION_LIMIT from 10k to 15k by @tomkinsc in #429
Full Changelog: v2.1.33.12...v2.1.33.13
v2.1.33.12
What's Changed
Full Changelog: v2.1.33.11...v2.1.33.12
v2.1.33.11
What's Changed
- incorporate assemble_refbased as refine/polish for denovo by @dpark01 in #422
- new metagenomic_denovo workflow by @dpark01 in #423
- consensus calling major_cutoff knobs and defaults by @dpark01 in #424
- update pangolin to pdata 1.9 by @dpark01 in #425
Full Changelog: v2.1.33.10...v2.1.33.11
v2.1.33.10
What's Changed
Minor functional updates
- CDC contractual updates to
sarscov2_illumina_full
(min coverage, genome name default prefix) - #419 - pangolin tasks: update_dbs_now invokes update data only (not pangolin software) - #420
Docker image updates only:
Full Changelog: v2.1.33.9...v2.1.33.10
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
Full Changelog: v2.1.33.8...v2.1.33.9