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Releases: broadinstitute/viral-pipelines

v2.3.6.0

23 Sep 12:40
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What's Changed

enterics related

assembly scaffolding & reference selection improvements

  • scaffold_and_refine_multitaxa -- more thorough assembly outputs by @dpark01 in #524
  • scaffolding and reference selection based on ANI by @dpark01 in #528
  • Reference selection improvements and nextclade generalization by @dpark01 in #529
  • scaffolding regression fixes plus docker updates by @dpark01 in #547
  • scaffold multitaxa: drop empty assembly output rows by @dpark01 in #554
  • report reference genome length in align_reads output; use this value for assemble_refbased. reference_genome_length by @tomkinsc in #538

demux_deplete and terra table data model updates

  • demux_deplete: make depletion optional, load biosample metadata to tables by @dpark01 in #551
  • demux_deplete small updates by @dpark01 in #552
  • demux_deplete fixes/updates by @dpark01 in #555

miscellaneous fixes and edge cases

  • allow additional options for picard in FastqToUBAM by @tomkinsc in #518
  • WDL code/style cleanups by @dpark01 in #523
  • expanded parameterization of align_and_count and additional output metrics by @tomkinsc in #525
  • guard against shell pipefails in align_and_count in instances where empty inputs would result in div-by-zero conditions by @tomkinsc in #535
  • classify_single: parameterize taxa to deplete by @dpark01 in #536
  • bugfix fetch_sra_to_bam by @tomkinsc in #542
  • Update polyphonia input parameters and defaults by @lakras in #545

docker container updates

build & CI related

Full Changelog: v2.2.4.0...v2.3.6.0

v2.2.4.0

17 Feb 00:18
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What's Changed

New workflows

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

Full Changelog: v2.1.33.17...v2.2.4.0

v2.1.33.17

27 Sep 14:49
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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

Full Changelog: v2.1.33.16...v2.1.33.17

v2.1.33.16

09 Mar 20:23
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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

Full Changelog: v2.1.33.15...v2.1.33.16

v2.1.33.15

21 Dec 19:15
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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

New Contributors

Full Changelog: v2.1.33.14...v2.1.33.15

v2.1.33.14

14 Sep 12:31
6f434e9
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What's Changed

Feature changes

  • task alignment_metrics: more resilient to large amplicon designs by @dpark01 in #435

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

11 Jul 14:40
7e90cb0
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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

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

09 Jun 02:25
2bfde65
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What's Changed

  • lofreq task portability, misc other edits by @dpark01 in #426

Full Changelog: v2.1.33.11...v2.1.33.12

v2.1.33.11

06 Jun 17:02
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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

18 May 14:59
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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