Merge pull request #121 from broadinstitute/dp-nextstrain

nextstrain wdl updates
broadinstitute · Jun 18, 2020 · 0ef4922 · 0ef4922
2 parents 0824c1b + ea9519b
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diff --git a/docs/workflows.rst b/docs/workflows.rst
@@ -4,10 +4,10 @@ WDL Workflows
 Documentation for each workflow is provided here. Although there are many workflows that serve different functions, some of the primary workflows we use most often include:
 
  - :doc:`demux_plus` (on every sequencing run)
- - :doc:`classify_krakenuniq` (included in demux_plus)
+ - :doc:`classify_multi` (metagenomics & host depletion)
  - :doc:`assemble_denovo` (for most viruses)
  - :doc:`assemble_refbased` (for less diverse viruses, such as those from single point source human outbreaks)
- - :doc:`build_augur_tree` (for nextstrain-based visualization of phylogeny)
+ - :doc:`augur_from_assemblies` (for nextstrain-based visualization of phylogeny)
  - :doc:`genbank` (for NCBI Genbank submission)
 
 .. toctree::