Bioinformatics Recipe Cookbook
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Your mission, should you choose to accept it, is to reproduce major findings of a Science paper in just 60 seconds.

This recipe is based on a fun diversion that I show during lectures. The goal of the recipe is to demonstrate that, when properly documented it is possible to reproduce major scienific findings with relative ease t and sometimes under a minute.

This recipe reproduces the main results published in the work:

On a properly set up system, and depending on bandwidth, the recipe completes under a minute. This includes getting the data, references, aligning and calling variants! The results even include annotations of the variant effects relative to the features on the genome.

The best way to enjoy this analysis is to have the following video playing while the analyis is running:

https://www.youtube.com/watch?v=yLo9k8Gifb0

You win and save the world if you can finish running the analysis before the music stops.

Note how this theme song makes even the otherwise bland analysis feel super exciting.

Recipe Code
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Recipe Interface
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Interface specification
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Double click on an element to insert it into the interface.
Integer values
                        [size]
                        label = "Window size"
                        display = "INTEGER"
                        value = 100
                        range = [1, 100]
                        help = "Selects the smoothing window."
                    
Float values
                        [cutoff]
                        label = "P_Value Cutoff"
                        display = "FLOAT"
                        value = 0.05
                        range = [0, 1]
                        help = "Selects the cutoff."
                    
Text box
                    [sra]
                    label = "Run Number"
                    display = "TEXTBOX"
                    value = "SRR519926"
                    regex = 'SRR\d+'
                    help = "Please provide SRR Run number"
                    
Dropdown menu
                    [color]
                    label = "Select color"
                    display = "DROPDOWN"
                    choices = [ ["R","Red"], ["B","Blue"] ]
                    value = "R"
                    help = "Select a color of your choice"
                    
Check box
                    [validate]
                    label = "Cross Validate"
                    display = "CHECKBOX"
                    value = true
                    help = "Apply cross validation on the results."
                    
Upload Field
                    [file]
                    label = "Upload a file "
                    display = "UPLOAD"
                    help = "Upload a file to analyze"
                    
Pick Data
                    [data]
                    label = "Pick data"
                    source = "PROJECT"
                    help = "Pick data from this project."
                    
Radio Buttons
                    [species]
                    label = "Select species"
                    display = "RADIO"
                    choices = [ ["c","Cat"], ["d","Dog"] ]
                    value = "c"
                    help = "Select the species."
                    
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Recipe display name
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A detailed explanation of what the recipe does (markdown OK).
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