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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 quality control for RNAseq raw reads, before the big steps of annotation quantification and differential expression.
  2. Run in a parallel/threating environment a pre-alignment quality control test for RNAseq.

Getting Started

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)

In future releases, Docker will simplify your use of QUARS, as there will no longer be necessary downloading individual packages (e.g. FastQC). Only Nextflow and Docker will be required.

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 --fastq_files '*.fastq.gz' --cpus 16

or

nextflow run https://github.com/TainVelasco-Luquez/QUARS  --fastq_files '*.fastq.gz' --cpus 16

Alternatively you can clone the repo and run it locally by

git clone https://github.com/TainVelasco-Luquez/QUARS
nextflow run QUARS/quars.nf  --fastq_files '*.fastq.gz' --cpus 16

If you are running on a cluster with HTCondor:

nextflow run TainVelasco-Luquez/QUARS --fastq_files '*.fastq.gz' --cpus 16 -profile condor

To modify memory, cpus and more options when running in clusters, go to nextflow.config.

Typical usage

  • For single end fastq files:

    nextflow run QUARS --fastq_files '*.fastq.gz' --cpus 16

    Which produces this Docs/QUARS_single.html

  • For paired end fastq files:

    nextflow run QUARS --fastq_files '*_{1,2}.fastq.gz' --singleEnd false --cpus 16

    Which produces this Docs/QUARS_paired.html

Timeline and report

In addition to the main QUARS.html report, QUARS also generates a processess execution timeline (see Docs/timeline_QUARS.html)) and an execution report, with a brief summary of the tasks and their consumption of computational resurces (see Docs/report_QUARS.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").
  • --cpus Integer specifying the number of cores to use. Be aware of the limits of your machine.

Options

  • --outdir Absolute path to the output data (must be enclosed in quotes). If no path specified, the default behaviour is to create in the current dir the folder "Results" (i.e. "./Results/").
  • -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.
  • --multiqc_config Input a .yaml file to configure multiqc title, comments, subtitles and more. if no supplied, then QUARS assumes is "./multiqc_config.yaml". Customisable items are fully described in MultiQC documentation.

Getting Help

nextflow run QUARS --help

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