MobiCT

ctDNA Analysis pipeline. Version 1.0.1

Table of Contents

• Introduction
• Quick Start
• Installation
  • Nextflow
  • Execution environment
    • Container platform
      • Docker
      • Singularity
    • Conda
• Usage
• Pipeline output
• Data availability

Introduction

Mobict is an analysis pipeline designed for detecting SNV and small InDels in circulating tumor DNA (ctDNA) obtained through non-invasive liquid biopsy, serving diagnostic, prognostic, and therapeutic purposes. The pipeline is built using Nextflow. The associated publication is available here: /doi/.../

Quick Start

1. Install nextflow (https://www.nextflow.io/docs/latest/install.html).

2. Create a conda environment for MobiCT:

   conda create -n myenv -c conda-forge -c bioconda gatk4 fgbio bwa fastp samtools picard vardict ensembl-vep

3. Download the reference genome

4. Download the datasets needed by VEP (see https://github.com/Ensembl/ensembl-vep)

5. Edit the .config file with input and output files/paths

6. Run MobiCT on your Dataset

   Nextflow -log /output_directory/my.log run MobiCT.nf -c nextflow.config

Installation

The prerequisites to run the pipeline are:

• Nextflow >= 22.04.0
• Docker or Singularity or conda

Nextflow

• Via conda

  See here

  conda create -n nextflow
  conda activate nextflow
  conda install bioconda::nextflow

• Manually

  See here

  Nextflow runs on most POSIX systems (Linux, macOS, etc) and can typically be installed by running these commands:

  # Make sure 11 or later is installed on your computer by using the command:
  java -version
  
  # Install Nextflow by entering this command in your terminal(it creates a file nextflow in the current dir):
  curl -s https://get.nextflow.io | bash 
  
  # Add Nextflow binary to your user's PATH:
  mv nextflow ~/bin/
  # OR system-wide installation:
  # sudo mv nextflow /usr/local/bin

Execution environment

Container platform

To run the workflow you will need a container platform: docker or singularity.

Docker

Please follow the instructions at the Docker website

Singularity

Please follow the instructions at the Singularity website

Conda

It is recommended to use a container platform. However, if you prefer to use Conda, please follow the instructions available here

Usage

Profile

To run the workflow you must select a profile according to the container platform you want to use:

• singularity, a profile using Singularity containers to run the softwares
• docker, a profile using Docker containers to run the softwares
• conda, a profile using conda environments to run the softwares

From Release

Default usage

The command will look like that:

nextflow run SimCab-CHU/MobiCT -r v1.0.0 -profile docker <rest of paramaters>

Test

nextflow run SimCab-CHU/MobiCT -r v1.0.0 -profile docker,test <rest of paramaters>

From repo

# clone the workflow repository
git clone https://github.com/SimCab-CHU/MobiCT.git

# Move in it
cd MobiCT

Default usage

# Run MobiCT
nextflow run MobiCT.nf -profile docker <rest of paramaters>

Test

# Run MobiCT
nextflow run MobiCT.nf -profile docker,test

Pipeline output

The output files are stored in the directory you specified using the outdir parameter in the .config file. The outdir contains a folder per sample plus a multiQC folder. Each sample folder contains a deduplicated and aligned .bam file and its index, an annotated .vcf file, 3 metrics files (.HsMetrics.1.txt, .HsMetrics.3.txt and QC.bcftools_stats.stats).

Data availability

Raw sequencing data (FASTQ files) of commercial controls used in the study are available @ https://www.ncbi.nlm.nih.gov/sra/PRJNA1209006.