v2.1.8.0

Update to Dockstore 1.9 API

• direct github apps based integration for all branch commits and tagged releases to viral-pipelines to Dockstore (skips viral-ngs-staging intermediary) using their latest API released a few days ago [#139, #140]

Workflow updates:

• fixes to NCBI Fetch_SRA_to_BAM [#138]
• new workflow classify_single (a single-sample version of classify_multi) [#133]
• new mafft_and_snp [#132, #133]
• replace all augur align calls with our own mafft invocation that is much faster [#132]
• augur_from_msa can take multiple keep_list inputs [#134]
• allow kraken2 task to take fasta input, not just bam (to allow for running on contigs) [#127]

Misc:

• various upstream docker image version updates [#126, #136, #137, #138]
• VM shape tuning [#128, #129]
• dxWDL update [#131]

v2.1.4.1

• assemble_refbased: additional stats output (num_read_groups, num_libraries, dist_to_ref_snps, dist_to_ref_indels) and more stringent default coverage requirements for run_discordance stats [#125]
• correct semantic versioning to match viral-core base version 2.1.4

v2.1.0.4

assemble_refbased workflow:

• default to minimap2 aligner instead of novoalign [#123, #110]
• add run_discordance task and output metrics for measuring discordance between sequencing runs within a sample [#124]
• disable ivar trim quality trimming due to unidirectional trim behavior (only run ivar trim for PCR primers) [#122]
• remove MultiQC from refbased workflow [#82]

metagenomics:

• bugfixes for kraken2 build [#120, #117]
• bugfixes for kaiju task [#113]
• remove blastx (optional) tasks from classify_multi [#102, #106]

BEAST (GPU):

• increase dnanexus runtime limit and specify dx_instance type [#116, #118]
• update docker image [#111]

nextstrain / phylogenetics:

• add snp-sites task to emit vcf files [#115]
• add augur mask step [#99]
• VM shape tuning [#112]
• rename and reorganize workflows a bit so they are all called augur_from_xxx [#121, #101]

miscellaneous:

• demux workflows: append lane number to bam filenames [#98, #100]
• update viral-core [#105, #124]
• update dxWDL [#103]

v2.1.0.2

• update nextstrain/base docker tag to build-20200529T044753Z [#95]
• add sequence counts (pre/post) as Int WDL task outputs for filter_subsample_sequences [#96]

v2.1.0.1

• update ncbi-tools docker image to tagged version with sra-tools v2.10.7
• bugfix: correct description parameter name for auger export

v2.1.0.0

• assemble_refbased changes [#83, #84]:
  • bugfix: workflows should never fail when no genome is produced. Empty output files are now properly emitted with no errors.
  • increase default min_coverage for consensus calling from 2 major allele reads to 3
  • bump ivar docker images to 1.2.2
  • update documentation
• build_augur_tree changes [#85, #90]
  • add augur clades task and integrate with main workflow
  • integrate existing augur filter task with main workflow
  • increase AUGUR_RECURSION_LIMIT to handle very deep/large trees
  • update documentation
• filter_bam_to_taxa bugfix for taxonomic_ids optional input [#92]
• add align_and_count_multiple_report for improved/bugfixed spike in count handling [#91]
• VM runtime reshaping [#88, #89, #92]
  • disable GCP preemption for certain long running tasks
  • expose disk size requirements for certain tasks and increase their default values
  • increase default RAM for rmdup_ubam task
• update viral-core (and downstream docker images) to v2.1.0

v2.0.21.5

• added vcf merging workflow and tasks (with snpEff annotation) [#61, #77]
• update dnanexus default kraken2 database [#80]
• Travis: bugfix for dockstore & viral-ngs-staging for tagged releases failing to sync [#78]
• Travis: reduce the number of CI tests for cromwell-on-local-travis instead of running the full set (for build speedups)
• update to viral-phylo 2.0.21.5
• genbank workflow updates [#79, #81]:
  • switch from mafft MSA-based alignment before annotation transfer to a scattered pairwise alignment prior to annotation transfer[#76]
  • add travis test coverage for both single-segment and multi-segment genomes to cover both code paths
  • RTD documentation updates

v2.0.21.4

• new workflows for beast: beast_gpu, beast_to_auspice [#66, #74]
• new workflows: subsample_by_metadata and newick_to_auspice [#68]
• Genbank: improved documentation of submission process and slight workflow updates [#51, #71, #75]
• Travis build: github staging / dockstore -- no longer tag non-master branch commits (and instead rely on unversioned branch labels) [#72]
• Travis build: update dxWDL 1.46.4 to 1.47 to reduce dxda file localization instability [#70]

v2.0.21.3

Travis CI fixes and tweaks

v2.0.21.2

Major changes:

• travis CI changes and cleanups, including new flattened-wdl deploy to github.com/broadinstitute/viral-ngs-staging [#62, #63]
• updates to nextstrain workflows: adds tasks for augur traits, augur filter, and inserts augur traits optionally into the main workflow [#59]
• metagenomics: addition of new workflows for classify_kraken2, classify_multi (which demonstrates kraken2-based human read depletion) as well as tasks for kraken2-based classification and database building, as well as blastx-based classification. Main workflows such as demux_plus or assemble_denovo have not yet changed default behavior until we get comfortable with the new workflows over various data sets. [#60]