zavolanlab / zarp-cli

A user-friendly command-line interface for the ZARP RNA-seq analysis workflow

Home Page:https://zavolanlab.github.io/zarp-cli/

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Implement initialization routine

mkatsanto opened this issue · comments

Is your feature request related to a problem? Please describe.
Upon running ZARP-cli for the first time (or whenever it is requested), users should be able to set up their own defaults, to be used for all subsequent runs, unless overridden by command-line parameters.

Describe the solution you'd like
An interactive session should be implemented in which a user provides defaults for the various user- and run-specific parameters. Descriptions of each parameter should be provided and a default suggested, read from a default config file shipped with ZARP-cli. Simply pressing for a given parameter should confirm the suggested default, otherwise the user's value is used. Values should be stored in a file ~/zarp/config.yaml. If the file is absent, such as when ZARP-cli was first started, the initiliazation routine should be automatically triggered. Alternatively, it should be triggered if the user provides the --init CLI flag. Whenever ZARP-cli is executed and the user config file is present, it should be used in any run unless specifically overridden by CLI parameters.

Blocked by #1, #2, #14 & #15