Update PhEval Pipeline Documentation #352
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souzadevinicius
requested review from
matentzn,
AO33,
kcortes133 and
yaseminbridges
and removed request for
kcortes133
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| ### Installing Jinja Template | ||
| The data preparation phase, checks the completeness of the disease, gene and variant input data and optionally preparing simulated VCF files if required, gives the user the ability to randomise phenotypic profiles using the PhEval corpus scramble command utility, allowing for the assessment of how well VGPAs handle noise and less specific phenotypic profiles when making predict. |
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I think you should clarify that the checking of the completeness of the disease, gene & variant input data is in fact checking the data contained in the phenopacket is complete for these fields. Also, maybe this paragraph could be split just so that it flows a bit better.
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| In resources folder, there is a file named *pheval-config.yaml*, this file is responsible for storing the PhEval Makefile generation. | ||
| - `data` property refers to the folder location where the necessary phenotypic data for the pipeline will be downloaded and extracted. |
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Is the data property specific to Exomiser? What will happen if it is left blank and users don't want to run Exomiser?
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I would say that the Pipeline docs all belong in the monarch_pheval repo? At the very least the About section should come before the Pipeline section as there is absolutely no context about what the pipeline is even for if someone is reading the docs through from the start. In fact, reading through the docs from the start still gives me no help in telling me how I might want to use PhEval or what it can do. A few simple examples in a logical set of steps explaining the library and the plugins to a complete beginner to lead them through to being able to write a plugin and execute a benchmark is what is needed. |
Fixes #351