/FLORA

workFLOw for Rnaseq analyses of the Amocyst project

Primary LanguageNextflowMIT LicenseMIT

FLORA: workFLOw for Rnaseq analyses of Amocyst project..

FLORA version Nextflow Developer

Introduction

FLORA is a FAIR scalable workflow allowing the analysis of RNAseq data of the AMOCYST project using state-of-the-art transcriptomics tools and statistical methods to conduct reproducible analyses using Nextflow. FLORA starts processing by correct RNAseq raw reads using Rcorrector. Then uncorrectable reads are removed using a Python script. rRNA contamination are also removed using Bowtie2 and the SILVA database before a quality filtering process of the reads using Trim Galore. Finally, the transcriptome assembly is performed using Trinity

The FLORA workflow is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It automates the mapping of an individual metagenomic sample on a concatenated reference. It is functional on DATARMOR (Ifremer computing cluster) and uses local dependencies.

Quick Start

i. Download the pipeline

git clone https://gitlab.ifremer.fr/cn7ab95/FLORA.git

iii. Run the workflow

Standard launch:

nextflow run main.nf

Custom launch on our supercomputer DATARMOR:

qsub run-main.nf

See usage docs for a complete description of all of the options available when running the pipeline.

Documentation

This workflow comes with documentation about the pipeline, found in the docs/ directory:

  1. Introduction
  2. Pipeline installation
  3. Running the pipeline
  4. Output
  5. Troubleshooting

Requirements

To use this workflow, it is necessary to:

  • complete the parameters defined in theconfig file
  • to have a SILVA database (SSU + LSU) indexed with Bowtie2
  • to create a file allowing to identify the condition and the replicate of each sample like the following example:
cond_A	cond_A_rep1	reads_A_rep1_R1.fq	reads_A_rep1_R2.fq
cond_A	cond_A_rep2	reads_A_rep2_R1.fq	reads_A_rep2_R2.fq
cond_B	cond_B_rep1	reads_B_rep1_R1.fq	reads_B_rep1_R2.fq
cond_B	cond_B_rep2	reads_B_rep2_R1.fq	reads_B_rep2_R2.fq

Credits

FLORA is written by Cyril NOEL, bioinformatics engineer at SeBiMER, the Bioinformatics Core Facility of IFREMER.

Support

For further information or help, don't hesitate to get in touch with the developper:

email