RNAseq-NF pipeline

A basic pipeline for quantification of genomic features from short read data implemented with Nextflow.

Requirements

• Unix-like operating system (Linux, macOS, etc)
• Java 11

Quickstart

1. If you don't have it already install Docker in your computer. Read more here.

2. Install Nextflow (version 23.04.0 or later):

    curl -s https://get.nextflow.io | bash
   

3. Launch the pipeline execution:

    ./nextflow run nextflow-io/rnaseq-nf -with-docker
   

4. When the execution completes open in your browser the report generated at the following path:

    results/multiqc_report.html 
   

You can see an example report at the following link.

Note: the very first time you execute it, it will take a few minutes to download the pipeline from this GitHub repository and the associated Docker images needed to execute the pipeline.

Pipeline flowchart

Here is a visual representation of the design of RNASeq-NF pipeline, generated using the visualization functionality of Nextflow.

%%{init: { 'theme': 'forest' } }%%
flowchart TD
    p0((Channel.fromFilePairs))
    p1(( ))
    p2[RNASEQ:INDEX]
    p3[RNASEQ:FASTQC]
    p4[RNASEQ:QUANT]
    p5([concat])
    p6([collect])
    p7(( ))
    p8[MULTIQC]
    p9(( ))
    p0 -->|read_pairs_ch| p3
    p1 -->|transcriptome| p2
    p2 --> p4
    p3 --> p5
    p0 -->|read_pairs_ch| p4
    p4 -->|pair_id| p5
    p5 --> p6
    p6 -->|$out0| p8
    p7 -->|config| p8
    p8 --> p9

Cluster support

RNASeq-NF execution relies on Nextflow framework which provides an abstraction between the pipeline functional logic and the underlying processing system.

This allows the execution of the pipeline in a single computer or in a HPC cluster without modifying it.

Currently the following resource manager platforms are supported:

• Univa Grid Engine (UGE)
• Platform LSF
• SLURM
• PBS/Torque

By default the pipeline is parallelized by spawning multiple threads in the machine where the script is launched.

To submit the execution to a UGE cluster create a file named nextflow.config in the directory where the pipeline is going to be executed with the following content:

process {
  executor='uge'
  queue='<queue name>'
}

To lean more about the avaible settings and the configuration file read the Nextflow documentation.

Components

RNASeq-NF uses the following software components and tools:

• Salmon
• FastQC
• MultiQC