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# Nextflow getting started

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## Before Getting Started

#### Windows Users
You should havve Windows Subsystem for Linux (WSL2) installed with a version of linux. My recommendation is that your version of linux should be `Ubuntu 20.04` because you will find more help online when you search for linux help. If you don't already have WSL2 installed, follow these directions to [install WSL2 on Windows 10](https://youtu.be/n-J9438Mv-s?t=51). Once you have a linux terminal open, you can follow any linux guide online because you are now using linux (as a virtual machine on your windows computer). Java is part of the default installation of Ubuntu 20.04 so you should be all set to install nextflow.

#### Mac Users
You will need to [install Java](https://devqa.io/brew-install-java/) because it's not part of the default installation of MacOS. To check if you installed Java previously, open a terminal window and type `java -version` and if you have it installed, you'll see which version is available.

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### Prerequisites
1. Java version 8 or later
- You can check by running `java -version` at the terminal. (If your output is `openjdk version 1.8.xxx` this is version 8. If you want to read more about why, here's a [link with more info](https://www.quora.com/Do-Java-1-8-and-Java-8-refer-to-the-same-thing).


### Installing Nextflow

1. Open a terminal window or (logon to `Xanadu`).
2. You should already be in your home directory but you can type `cd ~` or simply `cd` will also take you to your home directory.
3. Create a directory called `nextflow` and change directory to this new directory.
- `mkdir nextflow && cd nextflow`
4. Download and execute the nextflow install file by typing the following into your terminal.
- `curl -s https://get.nextflow.io | bash`

You can now run nextflow. Let's check the version by typing
- `./nextflow -version`.

But this is inconvenient because if you try to run nextflow from a different directory, you will need to type `~/nextflow/nextflow -version` so let's create a symlink so that we can use a shortcut. Type

- `sudo ln -s ~/nextflow/nextflow /usr/local/bin/`
- (on `Xanadu` you might not need to use `sudo`)

The `ln` command is a useful command to know so you might want to [read more about it](https://linuxize.com/post/how-to-create-symbolic-links-in-linux-using-the-ln-command/).

Now you can just type `nextflow -version` from any directory. Nextflow comes with a hello world pipeline ready to run so let's run our first pipeline!

- `nextflow run hello`

The output of your pipeline should be "hello world" four times each in a different language.

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