Skip to content

Make Report Specifications

Process Details

  • Name: make_report
  • Process UUID: f9314wh8mp0gm909kemwn25dkejhok
  • Process Group: Laava

Overview

This process generates comprehensive quality control reports for vector analysis workflows, producing both HTML and PDF formatted outputs with relevant quality metrics and analysis results. The process analyzes BAM files containing mapped sequencing reads and generates detailed reports including vector integration analysis, coverage statistics, and quality assessments.

This process is implemented in Bash, which invokes the make_report.sh script for report generation and analysis.

Key Functionality

  • Vector Annotation Processing: Handles both custom vector annotations and pre-defined BED files for ITR and mITR region analysis
  • Quality Metrics Generation: Computes coverage statistics, mapping quality, and vector-specific metrics
  • Multi-format Report Output: Generates both HTML and PDF versions of the comprehensive analysis report
  • Flipflop Sequence Analysis: Optionally incorporates flipflop FASTA sequences for enhanced vector characterization

Input/Output Specification

Inputs

Required Inputs

  • BAM File Set
    • Description: Set of BAM files containing aligned sequencing reads for analysis
    • Format: BAM

Optional Inputs

  • Flipflop FASTA

    • Description: FASTA file containing flipflop sequences for vector analysis
    • Format: FASTA

  • Vector BED

    • Description: BED file containing vector annotation coordinates for ITR and mITR regions
    • Format: BED

Outputs

  • Sample ID

    • Description: Sample identifier used throughout the analysis
    • Format: Sample ID value

  • Analysis TSV Files

    • Description: Multiple TSV files containing detailed analysis results and quality metrics
    • Format: TSV

  • Processed BAM Files

    • Description: BAM files with associated index files for downstream analysis
    • Format: BAM

  • BAM Index Files

    • Description: Index files (.bai) corresponding to the processed BAM files
    • Format: BAM_BAI

  • HTML Report

    • Description: Interactive HTML report containing comprehensive analysis results and visualizations
    • Format: HTML

  • PDF Report

    • Description: Static PDF version of the analysis report suitable for sharing and archival
    • Format: PDF

References & Resources

  • Tool Documentation: Contact the team for details on make_report.sh