# Welcome to Gtn: a containerized gc3pie app to run Tnseq pipeline

## Requirements

1. Docker

2. Root folder data structure:

  The root folder that contains the data to be analyzed is expected: 

  2.1 To have the following structure:

        root folder
        |-- group folders
            |--dataset folders
               |--fastq files

  2.2 To adhere to the following naming convention:

  A group/sample folder must be named as:
        
        g-{'group_name'}
    
  A dataset folder must be named as:

        d{number}-g-{'group_name'}
       
  2 FASTQ files for each dataset are expected to be named as:

        d{number}-g-{'group_name'}_R1.fastq
        d{number}-g-{'group_name'}_R2.fastq

  Example:

  This is a valid root folder (example_data) structure:

	example_data/
	├── g-control
	│   └── d1-g-control
	│       ├── d1-g-control_R1.fastq
	│       └── d1-g-control_R2.fastq
	└── g-treated
	     └── d1-g-treated
		├── d1-g-treated_R1.fastq
		└── d1-g-treated_R2.fastq
	
## Run gtn

###  Cloud infrastructure (UZH only)
 
```$ docker run -it -v /path/to/input/:/input -v /path/to/output/:/output -v /path/to/.ssh:/root/.ssh sparkvilla/tnseq```

### Localhost
```$ docker run -it -v /path/to/input/:/input -v /path/to/output/:/output sparkvilla/tnseq localhost```