nf-feelnc is a Nexflow pipeline for detection of lncRNA in reference and non reference genome annotation using feelnc program. It takes care of uncompressing genome and run the 3 feelnc scripts. This simple pipeline has been extracted and modified from TAGADA pipeline.

• Dependencies
• Usage
  • Nextflow options
  • Pipeline options
• Workflow
• Aknowledgments
• About

To use this pipeline you will need:

• Nextflow >= 21.04.1
• Docker >= 19.03.2 or Singularity >= 3.7.3

A small dataset is provided to test this pipeline. To try it out, use this command:

nextflow run sguizard/nf-feelnc -profile test,docker -revision 1.2

The pipeline is written in Nextflow, which provides the following default options:

For more Nextflow options, see Nextflow's documentation.

The pipeline executes the following processes:

1. Decompress annotations and/or genome files if its gziped.
2. Detect long non-coding transcripts with FEELnc.
   The annotation saved to results/annotation is updated with the results.
3. Aggregate quality controls into a report with MultiQC.
   The report is saved to results/control in a .html file.

Many thanks to Sarah Djebali (@sdjebali), Sylvain Foissac, Cervin Guyomar and Cyril Kurylo for their help and advices.

The GENE-SWitCH project has received funding from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No 817998.

This repository reflects only the listed contributors views. Neither the European Commission nor its Agency REA are responsible for any use that may be made of the information it contains.