Getting started: “How do I download this pipeline?”

Prerequisites
Installation
Running the Pipeline
1. Using nextflow run
  1. A. From Cloned Repository
  2. B. Directly from github
Updating the pipeline

Prerequisites

Before running the BactiSeq pipeline, ensure you have the following installed:

Core Requirements

Software	Minimum Version	Installation Guide
Java	8 or higher	OpenJDK or `sudo apt install openjdk-11-jre`
Nextflow	22.10.0	See installation methods below

Options for running the pipeline

The pipeline has been tested thoroughly with Singularity

Docker or Singularity - for containerized execution
Conda/Mamba - for dependency management

Optional but recommended

Git - for cloning the repository

Installation

Running the Pipeline

Using `nextflow run`

The nextflow run command is the primary way to execute Nextflow pipelines. You have several options:

A. From Cloned Repository

The BactiSeq pipeline is hosted on GitHub at sylvial-00/bactiseq. You need to clone it first:

# Clone the repository to your local machine
git clone https://github.com/sylvial-00/bactiseq.git
# Navigate to your cloned pipeline directory
cd bactiseq

# Run the pipeline
nextflow run main.nf -profile docker or singularity --input samplesheet.csv

# Or specify the config file explicitly
nextflow run -c nextflow.config --input samplesheet.csv

B. Directly from github

nextflow run https://github.com/sylvial-00/bactiseq --input samplesheet.csv

Updating the pipeline

# Navigate to your pipeline directory
cd /path/to/bactiseq

# Pull the latest changes from GitHub
git pull origin main

# If you're on a different branch
git pull origin develop  # or other branch name

# Then run with updates
nextflow run main.nf --profile docker --input samplesheet.csv

Getting started: “How do I download this pipeline?”

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