ReproHackathon_G6

Repository made for the ReproHackathon course of the Master 2 AMI2B program (Computational Biology) at Paris-Saclay University. The goal is to reproduce part of the results shown in : https://doi.org/10.1038/s41467-020-15966-7

Installation

1. Clone the repository

git clone https://github.com/raphaelrubrice/ReproHackathon_G6.git

2. Move to repository folder (optional)

cd ReproHackathon_G6

3. Run the pipeline (follow usage below)

PS : You can run the pipeline from anywhere on your device as long as you provide the relative path to the run.sh file.

Requirements

Make sure to have Nextflow and Docker up and running on your device. You must log into your docker account from the terminal before running the pipeline.

Usage

Here is how you can run the pipeline. --sra, --fasta_genome and --gff are mandatory arguments. The following command is the exact command you should run if you'd like to reproduce results from the paper cited above.

. run.sh --sra "SRR10379721,SRR10379722,SRR10379723,SRR10379724,SRR10379725,SRR10379726" --control "SRR10379724,SRR10379725,SRR10379726" --fasta_genome "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/013/425/GCF_000013425.1_ASM1342v1/GCF_000013425.1_ASM1342v1_genomic.fna.gz" --gff "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/013/425/GCF_000013425.1_ASM1342v1/GCF_000013425.1_ASM1342v1_genomic.gff.gz" -t 8

You can learn more about command parameters by running the command :

. run.sh -h

or

. run.sh --help