2022 Hackathon Project

Master M2 AMI2B - Universite Paris Saclay

Contributors :

• Ambre Baumann
• Lindsay Goulet
• George Marchment
• Clémence Sebe

This repository contains :

• The Nextflow workflow which performs the ARN-seq analysis
• The scripts from which are created the Docker Images
• The final report
• Documentation on how to run the workflow on a VM

Supervisors :

• Frédéric Lemoine
• Thomas Cokelaer

---

Dependencies to install

Run these commands to install Git, Singularity and Nextflow onto the VM.

Note : The VM used during the project was Biopipes (it is feasible that some of these dependencies are already installed, in the case of an other VM)

sudo apt install -y git-all
conda activate
mamba install -y  singularity=3.6.3
conda install -c bioconda -y nextflow
conda update -y nextflow

---

Run

To run the workflow, run the following commands :

conda activate
./run.sh

When running the workflow, the user can specify which processes they want to be executed (by default all the primary processes are all set to True, see run.sh).

Imagine the case, the user does not want to run the downloadFastqFiles process (to download the reads), but wants to use the ones which have already been downloaded (on a previous run), they would simply have to change the run.sh to :

#!/bin/bash

nextflow main.nf    \
    --downloadFastq false \
    --downloadGenome true \
    --downloadAnnotation true \
    --createGenome true \
    --doQuality false \
    --doTrimmomatic false \
    --getTrimmomatic false \
    --mapping true \
    --indexBam true \
    --countingReads true \
    --differentialAnalysis true

Note : The reads which are used in this case are the ones found in data/seqs/ and following the pattern 'SRR*_{1,2}.fastq'. If the user wants to use different fastqs, they would have to change the files parameter int the nextflow.config.

Note : In the same way, the user would have to modify the other parameters in the nextflow.config and run.sh for more flexibility, in the case they want to do a different analysis.

Here is a representation of the directed acyclic graph corresponding to the workflow :

---