v2.0.21.1

This new release:

• collapses a number of redundant workflow wdl files into a singular workflow with branching logic depending on user options -- in particular, all of assemble_denovo_*.wdl has been collapsed into assemble_denovo.wdl with options defining whether to deplete, call isnvs, etc.
• upgrade viral-core to 2.0.21, which removes unaligned read deduplication (via MVicuna) as a default pass from the taxonomic depletion step. A separate WDL task (task_read_utils.rmdup_ubam) is now provided to perform this function and is added into to various workflows (such as assemble_denovo*) where this is useful, but omitted from others (assemble_refbased, demux_plus) where it is not.
• adds a fastq_to_ubam workflow that converts paired or single-end fastq reads to an unmapped bam file with appropriate read group headers [#57]
• bug fixes to multiqc task to allow for multiple input files that share the same basename (but different directory paths) -- this is a common scenario for nextseq flowcells or any other scenario where the exact same libraries are sequenced on multiple lanes of a flowcell. [#58]
• slight updates to build_augur_tree workflow [#48]

v2.0.21.0

Updates:

• Convert all remaining WDL to v1.0 of language spec [#50, #53]
• Add WDL memory parameterization to all tasks [#43]
• Add multiqc in demux_plus and bugfix for execution on PAPI [#42, #54]
• Add new trimal task and workflows [#44]
• Rename spikein tasks and workflows to align_and_count [#55, #1]
• Bump viral-core to 2.0.21 -- includes illumina demux barcode counting optimization [#52]
• auto doc build on readthedocs works again [#47]
• Travis CI: re-enable cromwell tests and reorganize build stages a bit

v2.0.20.3

PR #41 -- adds continuous deploy to GCS, with updated documentation to reflect that.

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!