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A minimal NF pipeline

Based on but liter than RNAseq-NF, for pedagogical purpose.

Requirements

  • Unix-like operating system (Linux, macOS, etc)
  • Java 8

Quickstart

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

  2. Install Nextflow (version 0.24.x or higher):

     curl -s https://get.nextflow.io | bash
    
  3. Launch the pipeline execution:

     ./nextflow run gaow/fastqc-nf -with-docker
    
  4. When the execution completes open in your browser the report generated at the following path:

     results/multiqc_report.html 
    

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

Cluster support

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.

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