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Fastq Dump Collection Parser Specifications

Process Details

  • Name: fastq_dump_collection_parser
  • Process UUID: 874ds1596tqvdrnwcesmnqdvtohl8u
  • Process Group: Misc.

Overview

This process parses GEO (Gene Expression Omnibus) file information and user-entered sample names to create a structured CSV output that maps sample names to their corresponding file identifiers and metadata. It processes complex file naming structures that may include multiple lanes and paired-end sequencing files, organizing this information into a standardized format for downstream analysis workflows.

This process is implemented in Python.

Key Functionality

  • File Structure Parsing: Processes complex file naming patterns including multi-lane and paired-end sequencing data with nested delimiters
  • Metadata Integration: Combines sample names, GEO identifiers, directory paths, and collection types into a unified data structure
  • CSV Generation: Creates a structured output file with standardized column headers for easy integration with other bioinformatics tools

Input/Output Specification

Inputs

Optional Inputs

  • Backup Files
    • Description: Additional files that may be used as backup or reference data
    • Format: Any file format

Outputs

  • CSV Output
    • Description: Structured CSV file containing parsed sample information with columns for Name, GeoId, RemoteDir, and CollectionType
    • Format: CSV

Parameters & Settings

This process uses system parameters passed from the workflow environment and does not have user-configurable parameters in the Foundry UI.

References & Resources

  • Tool Documentation: Contact the team for details on the Python parsing script