This repository contains code of the docAlign pipeline, a Nextflow and Docker Version of MMSeq2 software tools for searching and clustering huge protein and nucleotide sequence sets.

• docAlign.nf - Nextflow pipeline implemeting the protein sequence search and alignment to a database
• Dockerfile - A docker file for building a docker image of the pipeline

Note: Ensure you have docker installed and running on your machine.

• Clone this repository: git clone https://github.com/Fredrick-Kakembo/docAlign.git
• cd docAlign
• Build the Docker image: docker build -t docAlign .

This will create a docker image of the pipeline called docAlign that will contain all the required dependencies required to run the pipeline. These include; conda, git, wget, MMSeq2, Nextflow.

Test your docker image: docker run dockAlign
This will run the docAlign search tool using the example sequence data provided along with the pipeline.

nextflow run docAlign.nf \
    --sequences /path/to/protein/sequences \
    --databases /path/to/database \
    --outdir <output Directory> \
    -with-docker docAlign

The --outdir option is optional. Default is results. It specifies the output directory. Also the path to the sequences and databases should be an absolute path, or specifying the ${PWD} before your inputs.

nextflow run docAlign.nf \
    --sequence ${PWD}/QUERY.fasta \
    --database ${PWD}/DB.fasta 
    --outdir Example 
    -with-docker docAlign