Clinical-Genomics
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  • Introduction
  • Documentation
    • Setup
    • References
    • Analysis
    • Parameters
    • Recipes
    • Code
      • Best Practise
      • Adding an env
    • API
      • Define Parameters
      • Download References
      • Identifiers
      • Initiation File
      • Install
      • IO
      • Modules
      • Path
      • Pedigree
      • QC metrics
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      • Subroutines
    • Cli
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  1. Documentation

Cli

PreviousSubroutines

Last updated 4 years ago

MIP uses to create a single command line interface (CLI) entry point to all MIP related processes. The main application is called by:

$ mip

This will show the usage, global parameters and all available commands and subcommands. There is currently three main commands:

  • Install

  • Analyse

    • rd_dna

    • rd_rna

    • rd_dna_vcf_rerun

  • Download

    • rd_dna

    • rd_rna

There are three levels of parameters:

  • Global

  • Commands

  • Sub commands

These parameters are defined for the CLI at each level of the underlying namespace in lib/MIP/Cli. The complete parameter feature is defined for each command and subcommand in definition file located under definitions.

A parameter that is unique to a command or subcommand should only be defined once in that namespace and corresponding definitions file.

A parameter that is shared by all subsequent processes only needs to be defined in the parent namespace and corresponding definitions file.

MooseX::App