WGS QC Workflow (Nextflow Version)

This is a Nextflow implementation of the WGS QC workflow for quality control and metrics collection of whole genome sequencing data.

Overview

The pipeline performs comprehensive quality control and metrics collection for whole genome sequencing data. It supports both BAM and CRAM input formats and can optionally convert the final BAM to CRAM format.

Architecture

graph TD
    subgraph Input
        A1[FASTQ R1] --> B[Fastp]
        A2[FASTQ R2] --> B
        C1[BAM/CRAM] --> D[Samtools]
        C2[Reference FASTA] --> D
    end

    subgraph Processing
        B --> E[Fastp Reports]
        D --> F[Processed BAM]
        F --> G1[Picard Multiple Metrics]
        F --> G2[Picard WGS Metrics]
        F --> H[Qualimap]
        F --> I[CRAM Conversion]
    end

    subgraph Output
        E --> J[MultiQC]
        G1 --> J
        G2 --> J
        H --> J
        I --> K[CRAM File]
        J --> L[Final Report]
    end

    style Input fill:#f9f,stroke:#333,stroke-width:2px
    style Processing fill:#bbf,stroke:#333,stroke-width:2px
    style Output fill:#bfb,stroke:#333,stroke-width:2px

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Requirements

• Nextflow 22.10.0 or later
• Docker
• Java 8 or later

Installation

1. Clone this repository:

git clone <repository-url>
cd <repository-directory>

2. Make sure Nextflow is installed:

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

Usage

The pipeline can be run using the following command:

nextflow run main.nf \
    --fastq_r1 "path/to/reads_R1.fastq.gz" \
    --fastq_r2 "path/to/reads_R2.fastq.gz" \
    --prefix "sample_name" \
    --fasta "path/to/reference.fasta" \
    --aligned_file "path/to/input.bam" \
    --cram false

Parameters

• --fastq_r1: Path to the first read file (R1) in FASTQ format
• --fastq_r2: Path to the second read file (R2) in FASTQ format
• --prefix: Sample prefix to be used in output creation
• --fasta: Path to the reference genome in FASTA format
• --aligned_file: Path to the input BAM or CRAM file
• --cram: Whether to convert final BAM to CRAM format (default: false)

Output

The pipeline generates the following outputs in the results directory:

• Fastp reports:
  • {prefix}_fastp.html
  • {prefix}_fastp.json
• Picard metrics:
  • Alignment summary metrics
  • Insert size metrics
  • Quality score distribution
  • Mean quality by cycle
  • Base distribution by cycle
  • WGS metrics
• Qualimap reports:
  • Coverage statistics
  • Mapping quality metrics
  • Insert size distribution
  • GC content analysis
• CRAM file (if --cram true):
  • {prefix}.cram
  • {prefix}.cram.crai
• MultiQC report:
  • {prefix}_multiqc_report.html
  • MultiQC data directory

Docker Containers

The pipeline uses the following Docker containers:

• staphb/fastp:latest for read quality control
• quay.io/biocontainers/samtools:1.21--h96c455f_1 for BAM/CRAM processing
• broadinstitute/picard:latest for metrics collection
• quay.io/biocontainers/qualimap:2.3--hdfd78af_0 for alignment quality assessment
• ewels/multiqc:latest for report generation

Reports

The pipeline generates several reports:

• pipeline_report.html: Pipeline execution report
• timeline_report.html: Timeline of pipeline execution
• trace.txt: Detailed execution trace

Directory Structure

results/
├── fastp/              # Fastp quality control reports
├── picard/            # Picard metrics
├── qualimap/          # Qualimap reports
├── cram/              # CRAM files (if --cram true)
└── multiqc/           # MultiQC report and data

License

This project is licensed under the terms of the license included in the repository.

Author

George Carvalho ([email protected])