Metagenomics - Pipeline

In this project we built a metagenomics-pipeline.

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.

Prerequisites

Qiime2 does not currently support Windows.

In case a windows platform is required, we recommend using Windows Subsystem for Linux or Virtual Machines

Installing

Download and install the latest version of miniconda:

curl -O -L https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

Add the correct channels in the conda (so that it knows where to look for packages):

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Install (and activate) Qiime2 within a conda enviroment:

wget https://data.qiime2.org/distro/core/qiime2-2019.7-py36-linux-conda.yml
conda env create -n qiime2-2019.7 --file qiime2-2019.7-py36-linux-conda.yml

Install CWL tool into Qiime2 enviroment:

conda install -c bioconda cwltool

Install required tools into Qiime2 enviroment:

conda install -c bioconda fastqc trim-galore

In case R is not installed in Qiime2 enviroment, please follow the instructions found here: https://cran.r-project.org/bin/linux/ubuntu/README.html The following packages are required in order for the R scripts, which are used in the pipelines, to run properly:

Documentation

For the Common Workflow Language please find instructions here: https://www.commonwl.org/user_guide/

Directories:

R_scripts folder contains all R scripts which can be used from the pipeline created
mapping folder contains all metadata files
workflows folder contains all pipelines which have been created
wrappers folder contains all wrappers which are used from the workflows
yaml_files folder contains all YAML files that are used as input for the pipelines

Usage

Create a new directory and place all fastq files in it
Create a metadata file (see mapping/manifest for an example)
Import your data as a Qiime2 artifact
Create a new classifier or use a pre-trained one
Give all paths of your files and any other desirable input in yaml_files/fastqc_trim_qiime2.yml

Run the following command:

cwl-runner workflows/fastqc_trim_qiime2.cwl yaml_files/fastqc_trim_qiime2.yml

License

This project is licensed under the GNU General Public License v3.0 - see the LICENSE file for details