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broadinstitute / viral-pipelines

viral-ngs: complete pipelines
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Enhancing documentation for viral-pipelines #461

Closed golu099 closed 1 year ago

golu099 commented 1 year ago

Adding documentation to important input/ouput parameters for some of the more used workflows in the pipeline (assembled_refbased, demux_deplete,classify_single, augur_from_assemblies, and genbank.

Additionally orphan workflows will be noted.

dpark01 commented 1 year ago

One quick note: I went into readthedocs and activated automatic public builds of the fnegrete_test branch so we can check there for how things render as you edit this PR.

See here for rendered output: https://viral-pipelines.readthedocs.io/en/fnegrete_test/

See here for build status (right now it's succeeding so nothing to see here, but if for some reason you had a syntax error or something, you'd see failures here): https://readthedocs.org/projects/viral-pipelines/builds/

golu099 commented 1 year ago

Did we merge this? Should I keep it open for future documentation fixes?

golu099 commented 1 year ago

amplicon16S analysis wdl renamed to classify_qiime2_multi

Noticed that the old name is on the master branch still, so we should updated this