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Trimmer Summary Specifications

Process Details

  • Name: Trimmer Summary
  • Process UUID: 17fc808a-e169-11e9-be30-e0aab38271b1
  • Process Group: Summary

Overview

This process parses Trimmomatic trimmer removal log files and creates a summary table for reporting purposes. It extracts read count statistics from trimming operations and generates a consolidated TSV file containing input and output read counts for each sample processed through the trimming workflow.

This process is implemented in Perl.

Key Functionality

  • Log File Parsing: Extracts read count statistics from fastx_trimmer log files
  • Data Aggregation: Consolidates trimming statistics across multiple samples into a single summary table
  • Report Generation: Creates a structured TSV file with total reads and reads remaining after trimming for each sample

Input/Output Specification

Inputs

Required Inputs

  • Log File

    • Description: Trimmomatic trimmer removal log file containing read processing statistics
    • Format: log

  • Mate

    • Description: Mate pair information for the sequencing data
    • Format: mate

Outputs

  • Output File TSV
    • Description: Summary table containing trimming statistics with total reads and reads after trimming for each sample
    • 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 the Perl script implementation