Your Project Name

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Overview

This project uses Nextflow for workflow management and Apptainer (formerly Singularity) for containerized execution to ensure reproducibility and portability of bioinformatics analyses.

The pipeline includes running MrBayes for phylogenetic analysis using containerized environments managed seamlessly by Nextflow.

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Table of Contents

• Prerequisites
  
• Installation
  
  • Java
    
  • Nextflow
    
  • Apptainer
    
• Configuration
  
• Running the Pipeline
  
• Pipeline Structure
  
• License
  
• Contact
  

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Prerequisites

• Linux operating system (tested on Ubuntu 20.04+)
• Java 17 or later
• Bash shell
• Internet access for container downloads

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Installation

Java

Ensure Java 17 or later is installed:

java -version

If not installed, on Ubuntu:

sudo apt update sudo apt install openjdk-17-jdk

Nextflow

Install Nextflow via official installer script:

curl -s https://get.nextflow.io | bash

mv nextflow ~/bin/

or any directory in your $PATH

Verify:

nextflow -version

Apptainer

Apptainer replaces Singularity with active support and fixes.

Remove any conflicting Singularity packages:

sudo apt-get remove --purge singularity-container sudo apt --fix-broken install

Download Apptainer .deb packages

Get the latest version from Apptainer releases, for example:

apptainer1.4.1amd64.deb

apptainer-suid1.4.1amd64.deb

Install packages:

sudo dpkg -i apptainer_1.4.1_amd64.deb apptainer-suid_1.4.1_amd64.deb

Configure Apptainer

Create config directory and config files with proper permissions:

``` sudo mkdir -p /etc/apptainer sudo tee /etc/apptainer/apptainer.conf > /dev/null <<EOF allow setuid = yes enable overlay = yes mount proc = yes mount sys = yes mount dev = yes mount devpts = yes mount home = yes mount tmp = yes mount hostfs = yes EOF

sudo touch /etc/apptainer/capability.json /etc/apptainer/ecl.toml sudo chown root:root /etc/apptainer/{capability.json,ecl.toml} sudo chmod 644 /etc/apptainer/{capability.json,ecl.toml} ```

Test Apptainer

apptainer exec docker://alpine echo "Hello Apptainer"

Configuration

Configure Nextflow to enable Apptainer container support by editing nextflow.config:

``` singularity { enabled = true autoMounts = true cacheDir = "$PWD/singularity" // path = '/usr/bin/apptainer' // uncomment if Apptainer not in PATH }

process { withName: mrbayes { container = "$HOME/.singularity/images/mrbayes_3.2.7.sif" cpus = 2 memory = '2 GB' time = '1h' } }

```

Optional: Pre-pull container images for faster startup and fewer runtime errors:

mkdir -p ~/.singularity/images apptainer pull ~/.singularity/images/mrbayes_3.2.7.sif docker://quay.io/biocontainers/mrbayes:3.2.7--h760cbc2_0

Running the Pipeline

Run your pipeline with Nextflow:

nextflow run main.nf -with-singularity

Or specify the container image manually if needed:

nextflow run main.nf -with-singularity $HOME/.singularity/images/mrbayes_3.2.7.sif