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nextstrain wdl updates #121

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merged 9 commits into from
Jun 18, 2020
Merged

nextstrain wdl updates #121

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2140b8c
change cpu load avg to float, figure out output filenames more automa…
dpark01 Jun 12, 2020
96b5a65
more cpu for refine and ancestral tree
dpark01 Jun 12, 2020
eac00f5
report full cpu load string
dpark01 Jun 12, 2020
95bb73b
more vm reshaping
dpark01 Jun 13, 2020
035e055
increase ancestral_traits for profiling
dpark01 Jun 13, 2020
fcce5f2
fix snp-sites call to make compliant vcf, rename build_augur_tree to …
dpark01 Jun 15, 2020
dc8d8ec
rename beast_to_auspice to augur_from_beast_mcc
dpark01 Jun 15, 2020
2929aee
fix ram output int for task augur_import_beast; add set -e (and somet…
dpark01 Jun 15, 2020
ea9519b
more reshaping
dpark01 Jun 16, 2020
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4 changes: 2 additions & 2 deletions docs/workflows.rst
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Expand Up @@ -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::
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