README.md

# 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 (local computer)

1. Open a terminal window.
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/` 
    
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/).

### Installing Nextflow on Xanadu
1. Start an interactive session to keep the admins happy.
    - `srun -p general -q general -t 4:00:00 --mem 4G --pty bash`
2. Create an `opt` directory in your home directory and change directory into this new directory.
    - `mkdir -p ~/opt && cd ~/opt`   
3. Download and install the nextflow install script.
    - `curl -s https://get.nextflow.io | bash`

Add the path to the `opt` directory to your `PATH`

4. Open your `.bashrc` file using `vim` or `nano`.
    - `vim ~/.bashrc`
6. Add the following line to the end of your `.bashrc` file.
    - `export PATH="/home/FCAM/$USER/opt/:$PATH"`
7. Source your `.bashrc` so the change takes effect.
    - `source ~/.bashrc`
8. Check if the new `opt` directory is in your `PATH`.
    - `echo $PATH | grep "$USER/opt"`
    - You should see your username and opt in red

### Running Nextflow

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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### Running Nextflow RNAtoy pipeline on Xanadu

If you haven't already done so, start an interactive session `srun -p general -q general -t 4:00:00 -c 4 --mem 8G --pty bash`

1. Create a `nextflow_pipelines` directory in your home directory and change into this directory
    - `mkdir -p ~/nextflow_pipelines && cd ~/nextflow_pipelines`
2. Clone the `rnatoy` repo and change into this direcotry.
    - `git clone https://github.com/nextflow-io/rnatoy.git && cd rnatoy`
3. Load singularity
    - `module load singularity`
4. Pull the needed docker container
    - `singularity pull docker://nextflow/rnatoy:1.3`
5. Run the rnatoy pipeline using a singularity container
    - `nextflow run main.nf -with-singularity rnatoy_1.3.sif`