v2.0.20.2

add merged krona reports (#40) to krakenuniq task and demux_plus workflow

v2.0.20.1

This release includes some updates to the CI build, to reference based assembly workflows, and adds nextstrain workflows, along with other smaller tweaks.

• add nextstrain augur workflow (#39)
• add bams_multiqc workflow (#34)
• improvements and updates to refbased assembly workflow, including accepting multiple bams per sample at input, scattering alignment jobs by bam, and merging and reheadering as needed (#33, #36)
• VM tuning (#37, #31, #29)
• update viral-core to 2.0.20.1
• update viral-assemble to 2.0.17.0
• changes to Travis CI build structure, with increased reliance on miniwdl (#38)

v2.0.17.0

• Bump viral-core and viral-assemble to v2.0.17.0, updates Picard and Novoalign, among other things
• Modernize assemble_ref_based workflow and incorporate iVar primer trimming
• Add MultiQC into WDL workflows
• Tune VM/instance shapes for demux
• Parallelize post-demux fastqc runs

v2.0.15.0

Merge pull request #17 from mlin/mlin-fix-Fetch_SRA_to_BAM

fix Fetch_SRA_to_BAM use of $PLATFORM

v2.0.11.0

Very first working version post-refactor!