run_nf-core-taxprofiler

Automation script for running the pipeline nf-core/taxprofiler

nf-core/taxprofiler is a bioinformatics best-practice analysis pipeline for taxonomic classification and profiling of shotgun metagenomic data.

It allows for in-parallel taxonomic identification of reads or taxonomic abundance estimation with multiple classification and profiling tools against multiple databases, produces standardised output tables.

Find more information here: https://nf-co.re/taxprofiler/1.1.2

This project is a automation script to create the input files needed to run the pipeline nf-core/taxprofiler.

Description

The project contains two files:

• The main script run_taxprofiler.sh allows the execution of the python files and the nf-core/taxprofiler pipeline
• The folder scripts containing the following python scripts:
  • Samplesheet_generator.py : to generate the samplesheet
  • Database_generator.py : to generate the database samplesheet

The main script run_taxprofiler.sh takes two positionnal arguments:

• The path to the directory containing your fastq files
• The profiling tools you want to use for the analysis. Here are the options:
  • Kraken2,
  • Bracken, KrakenUniq,
  • MetaPhlan3,
  • Malt,
  • DIAMOND,
  • Centrifuge,
  • Kaiju &
  • mOTUs depending on what you are analyzing.

Samplesheet_generator.py takes the list of samples, the sequencing technology (ILLUMINA or NANOPORE) and returns a samplesheet: samplesheet.csv

Database_generator.py takes a chain of profiling tools as argument and return the database samplesheet: database.csv

Usage

Pull the repository

git pull https://github.com/Maryemt/run_taxprofiler.git

Once it is done

chmod +x run_taxprofiler.sh scripts/*

Execute the pipeline

./run_taxprofiler.sh  data_directory/ <TOOL1>,<TOOL2>

Where

• data_directory is the path to the file containing your fastq files
• TOOL1,TOOL2... is the list of the profilers you want to use during the analysis

Example :

./run_taxprofiler.sh  data/ centrifuge,kraken2

Contact

If you found an issue or would like to submit an improvment to this project , you can contact me via LinkedIn or by email (khoudiathiampro@gmail.com)