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Concat Fastqs Specifications

Process Details

  • Name: concat_fastqs
  • Process UUID: f931s98wjmt58prmr8fod1s5ptmgdn
  • Process Group: Annotation

Overview

This process concatenates paired-end FASTQ files into a single merged file. It takes two paired-end sequencing read files and combines them sequentially, which can be useful for downstream analyses that require single-file input or for consolidating data from multiple sequencing runs.

This process is implemented in Groovy, which invokes Bash commands for file concatenation operations.

Key Functionality

  • File Concatenation: Merges two paired-end FASTQ files into a single output file
  • Directory Management: Creates a dedicated output directory (mmseqs) for organized file storage
  • Paired-End Processing: Handles standard paired-end sequencing data formats

Input/Output Specification

Inputs

Required Inputs

  • Reads

    • Description: Set of paired-end FASTQ files to be concatenated
    • Format: FASTQ

  • Mate

    • Description: Mate pair identifier for paired-end read processing
    • Format: Mate

Outputs

  • Reads
    • Description: Single concatenated FASTQ file containing merged paired-end reads
    • Format: FASTQ

Parameters & Settings

This process uses default concatenation parameters and does not expose user-configurable settings in the Foundry UI.

References & Resources

  • Tool Documentation: Standard Unix cat command for file concatenation