Skip to content

v2.1.18.0
Compare
Choose a tag to compare
@dpark01 dpark01 released this 17 Jan 00:59
· 1701 commits to master since this release
v2.1.18.0
799e054
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Learn about vigilant mode.

New general workflows:

  • new workflow demux_deplete. This sits between demux_only (demux and fastqc) and demux_plus (which adds kraken, spades, etc) and just does demux, fastqc, and depletion. If optionally given "augmented" samplesheets and NCBI BioSample mappings, it will produce SRA submission bundles as well. [#191]
  • new workflow mafft_and_snp_annotated, which adds snpEff annotation to the snp-sites output [#194]

New SARS-CoV-2 specific workflows. Up until this release, all included workflows were generally applicable to most viral taxa. This release includes a number of single-taxon workflows exclusively for SARS-CoV-2 in order to increase efficiency for high throughput work on this one virus.

  • new workflow sarscov2_illumina_full is a full end-to-end workflow from Illumina BCL tarball through Genbank, SRA, and GISAID submission bundles. It wraps together demux_deplete, assemble_refbased, sarscov2_lineages, sarscov2_genbank. It requires the user to pre-register NCBI BioSample entries and to provide an "augmented" samplesheet for demux. [#191, #196]

  • new workflow sarscov2_genbank. Prepares single-segmented genome assemblies for submission to NCBI Genbank using their new SARS-CoV-2 submission mechanism (which may become more mainstream for other viruses as well). Incorporates the new VADR (Viral Annotation DefineR) tool from NCBI to annotate (produce tbl files) and QC (flag frameshift and other problems) using the same settings that Genbank uses for QC -- this filters out genomes from submission that fail VADR QC and should result in Genbank submissions with no rejections. [#191]

  • new workflow sarscov2_lineages and sarscov2_nextclade_multi. Runs Nextclade and Pangolin to do lineage/clade classification on SARS-CoV-2 genomes. [#184, #185, #186]

  • nextstrain/augur workflow improvements and bugfixes to allow for merging of multiple metadata tsv files. This simplifies the process of regular builds where some data is changing frequently [#189, #181, #191]

  • docker image updates: [#195, #190, #187, #182, #191, #193]

  • VM shape updates [#188]

  • README update with diagram [#183, @llangit-broad]

Assets 2
Loading