ajodeh-juma/ngs-academy-africa-nfcore

Advanced Training in Bioinformatics Workflows: Beginner - Intermediate level Bioinformaticians working with next-generation sequencing data in East-Africa. - Introduction - Login - Prep - Your First script - Simple RNA-Seq pipeline ## Introduction This lesson is an introduction to the workflow manager Nextflow, and nf-core, a community effort to collect a curated set of analysis pipelines built using Nextflow. Nextflow enables scalable and reproducible scientific workflows using software containers such as Docker and Singularity. It allows the adaptation of pipelines written in the most common scripting languages such as R and Python. Nextflow is a Domain Specific Language (DSL) that simplifies the implementation and the deployment of complex parallel and reactive workflows on clouds and clusters. This lesson motivates the use of Nextflow and nf-core as a development tool for building and sharing computational pipelines that facilitate reproducible (data) science workflows. ## Login From the terminal of your local computer, you can log into the HPC using the following command line, followed by pressing . You will be prompted to type in your password. On a Linux system, you can use the `Ctrl-Alt-T` keyboard shortcut to open a terminal. ``` ssh @172.16.13.171 ``` If using PuTTY, type `172.16.13.171` in the `Host Name (or IP address)` field and `open` the program. Login with user name when prompted and key in your password. ## Prep In your `home` directory, follow the steps: Clone the repo in your `home` directory ``` git clone github.com ``` ## Your first script 1. Open your first nextflow script `wc.nf` using your favourite text editor (`nano` or `vim`) 2. Run the script using `nextflow` ``` nextflow run wc.nf ``` 2. Create a `process` in the script to `print` the number of reads in the input file provided. Ensure that you capture the `output` as `stdout` **Quiz:** *How many reads are in the input file?* --- Answer --- ## Simple RNA-Seq pipeline ### Using Conda/Bioconda 1. Create a `conda` environment ``` conda env create -f environment.yaml ``` The …