Reproducible Pipelines

Pre-built analysis pipelines for cancer research.

GATK Variant Calling Pipeline

Overview

Complete pipeline for germline and somatic variant calling using GATK best practices.

Components

• BWA-MEM - Read alignment
• GATK - Variant calling
• VEP - Variant annotation
• QC - Quality control metrics

Usage

# Run the pipeline
nextflow run hack-cancer/gatk-variant-calling \
  --input samples.csv \
  --reference hg38.fa \
  --output results/

Outputs

• VCF - Variant calls
• BAM - Aligned reads
• QC - Quality metrics
• Reports - HTML reports

RNA-seq Analysis Pipeline

Overview

Differential gene expression analysis for cancer samples.

Components

• STAR - Read alignment
• featureCounts - Read counting
• DESeq2 - Differential expression
• GSEA - Pathway analysis

Usage

# Run the pipeline
nextflow run hack-cancer/rnaseq-analysis \
  --input samples.csv \
  --reference hg38.fa \
  --gtf genes.gtf \
  --output results/

Single Cell Analysis Pipeline

Overview

Complete single-cell RNA-seq analysis workflow.

Components

• CellRanger - Read processing
• Seurat - Quality control
• Monocle3 - Trajectory analysis
• CellChat - Cell communication

Usage

# Run the pipeline
nextflow run hack-cancer/single-cell-analysis \
  --input samples.csv \
  --reference hg38.fa \
  --output results/

Cloud Deployment

Google Cloud

• Terraform - Infrastructure as code
• Kubernetes - Container orchestration
• Cloud Storage - Data storage

AWS

• CloudFormation - Infrastructure
• ECS - Container service
• S3 - Object storage

Reproducibility

• Docker - Containerization
• Conda - Environment management
• Nextflow - Workflow orchestration
• Git - Version control