pipelineAlignment

A Nextflow-based genomic alignment pipeline.

📦 Repository Structure

.
├── 1OrionPax.nf                # Main workflow file 1
├── 2Mirage.nf                  # Main workflow file 2
├── autobots.pbs                # PBS job script
├── megatron.config             # Pipeline configuration
├── modules/                    # Nextflow submodules
│   ├── local/                  # Custom processes
│   └── sampleSheets/           # Input CSVs
└── starscream.pbs              # PBS job script

🚀 Quick Start

1. Install dependencies:

   conda install -c bioconda nextflow

2. Run the pipeline:

   nextflow run 1OrionPax.nf -c megatron.config

⚙️ Configuration

Edit megatron.config for:

• Input/output paths
• Resource allocation (CPU/memory)
• Reference genomes

📝 Sample Sheets

Format your input CSV in modules/sampleSheets/: Add directory and .csv

sample,fastq
sample1,/path/to/reads_R1.fastq.gz

🤖 PBS Job Submission

qsub autobots.pbs

📌 Requirements

• Nextflow ≥22.04
• Java 8+
• Singularity/Docker (recommended)

Acknowledgement:

This pipeline was developed with resources from the Univeristy of Stellenbosch