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Parse Dnadiff Specifications

Process Details

  • Name: parse_dnadiff
  • Process UUID: f931t9jpmbxorfay4vwrdtxgbdfve7
  • Process Group: MAG-qc

Overview

This process parses dnadiff reports to extract relevant genomic differences into a standardized TSV format. It is designed to process multiple dnadiff output files in parallel, converting the text-based reports into structured tabular data suitable for downstream analysis and quality control of metagenome-assembled genomes (MAGs).

This process is implemented in Bash, which invokes a Python script for parsing the dnadiff reports.

Key Functionality

  • Parallel Processing: Processes multiple dnadiff report files simultaneously using background processes
  • Format Conversion: Converts dnadiff text reports into structured TSV format for easier data manipulation
  • File Organization: Creates organized directory structure for output files based on input paths
  • Batch Processing: Handles sets of input files efficiently with automated basename extraction

Input/Output Specification

Inputs

Required Inputs

  • OutTXTset
    • Description: Set of dnadiff report files in text format containing genomic comparison results
    • Format: TXT

Outputs

  • outputFileTSV
    • Description: Parsed dnadiff results in tabular format with extracted genomic differences and statistics
    • Format: TSV

Parameters & Settings

This process does not have user-configurable parameters in the Foundry UI.

References & Resources

  • Tool Documentation: Contact the team for details on parse_dnadiff.py