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UPHL-BioNGS / Cecret

Reference-based consensus creation
MIT License
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creation of a parameter schema #99

Closed k-florek closed 1 year ago

k-florek commented 2 years ago

All nf-core workflows include a json parameter schema file in the top level directory that outlines all of the parameters of the workflow. Here are some examples: viralrecon
mycosnp
bactopia

nf-core includes a tool to help with creating the file if you are using nf-core schema builder.

StaPH-B Toolkit v2 will use this file to tell users which parameters can be supplied with each workflow. If there isn't a schema file the toolkit will just inform the user that help is not available for this workflow. Including this file for Cecret will be really helpful for users once I release v2 of the toolkit.

erinyoung commented 2 years ago

I won't be able be able to move Cecret v.3.0.20220520 to the staphB toolkit with the current layout of the staphB toolkit.

I'm currently satisfied in defining all the params in the nextflow workflow scripts and a config file for a couple of reasons, one of which is time constraints.

I'm looking forward to the next version of the staphB toolkit.

erinyoung commented 1 year ago

This has, in theory, been added with https://github.com/UPHL-BioNGS/Cecret/pull/111.

Let me know if it's not up to snuff.