kevinsayers / quars

QUAlity control for RNA_Seq, a nextflow pipeline

Welcome to QUARS ~ QUAlity control for RNA_Seq

QUARS creates a MultiQC report out of the FastQC and Fastp results of both single and paired end RNAseq raw reads (.fq and simmilars). Powered by Nextflow.

Motivation

If like me, you have waited several hours or days for some RNAseq pipelines to finish, just to realise that the initial quality control step required further trimming! or simply that my raw reads were so bad they need to be excluded from further analysis. Then, like me, you will enjoy QUARS.

QUARS is an attemp to:

1. Make only a quality control of RNAseq raw reads, before the big steps of annotation quantification and differential expression.
2. Run in a parallel/threating environment quality control of RNAseq.

Getting Started

So you have decided to use QUARS, here is what you'll need

Prerequisites

QUARS builds upon

• Nextflow (< version 0.30.2 build 4867).

And supported for now,

• fastp (< 0.18.0)
• fastQC (< v0.11.7)
• multiQC (< v1.6.dev0)

Installation

Integration with Docker is in progress.

Thanks to nextflow. installation is not a must, you just have to call it from command line as:

nextflow run TainVelasco-Luquez/quars.nf

or

nextflow run https://github.com/TainVelasco-Luquez/quars.nf

Alternatively you can clone the repo and run it locally by

git clone https://github.com/TainVelasco-Luquez/QUARS
nextflow run TainVelasco-Luquez/quars.nf

If you are running on a cluster:

nextflow run TainVelasco-Luquez/quars.nf -profile condor

Typical usage

• For paired end fastq files:

  nextflow run quars.nf --fastq_files 'mydir/*.fastq.gz'
  

  Which produces this multiqc_report_paired.html

• For single end fastq files:

  nextflow run quars.nf --fastq_files 'mydir/*_{1,2}.fastq.gz' --singleEnd false
  

  Which produces this multiqc_report_single.html

Arguments

--fastq_files Absolute path to input .fastq data (must be enclosed with single quotes). If no path specified, the default behaviour is search in the current dir for the folder "Data" (i.e. "./Data/") --singleEnd Logical indicating whether the files are single ("true". This is the default beahaviour) or paired end ("false").

Options

--outdir Absolute path to the output data (must be enclosed in quotes). If no path specified, the default behaviour is search in the current dir for the folder "Results" (i.e. "./Results/"). Be sure to add the final "/" to the path. --cpus Integer specifying the number of cores to use. Be aware of the limits of your machine. -profile condor Used when in a cluster with the HTCondor executor. For configuration of the HTCondor parameters go to nextflow.config and change the required settings.

Credits

@TainVelasco-Luquez QUARS is heavily influenced by the NGI-RNAseq pipeline, whose author, @ewels solved questions and provide ideas through his code. This work was developed for the Grupo de Investigación en Terapia Celular y Molecular from the Pontificia Universidad Javeriana.

Licence

This project is licensed under the MIT License - see the LICENSE.md file for details