Workflow_Excercise2

This pipeline is to process a workflow on bacteria raw sequence data. The following diagram shows how this workflow works. Firstly we will take raw paired sequence data into FastP to trim the data. FastQC is implemented before and after FastP to monitor the trimming process. The trimmed data will be assembled using Skesa. After Skesa, QUAST and MLST will be conducted parallel.

Step 1: Create an environment that contains the required tools for this pipeline

Download the .yml file in this repo, and run the following code to build the environment

conda env create -n <ENVNAME> --file ENV.yml

Or you can also manually download all the required tools

conda create -n <ENVNAME>
conda install -c bioconda -c conda-forge fastqc fastp skesa quast mlst
conda activate -n <ENVNAME>

Then you will need to install Nextflow in the environment you previously built using conda with the following command:

conda install nextflow

Step 2: Running main.nf file

Download the main.nf file in this repo.

To execute main.nf, You need to replace the directory in the first line in the main.nf file with your current directory.

After changing the directory you can execute main.nf with code below:

nextflow run main.nf

Step 3: Viewing results

In your current directory, there will be a results folder, and in the results folder, there are the following folders with corresponding result files:

• FastQC_PreTrim
• FastP
• FastQC_PostTrim
• SKESA
• QUAST
• MLST