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Spatial Processing Dataset Specifications

Process Details

  • Name: Spatial Processing Dataset
  • Process UUID: jbf4gy8pf6yb7a51lui1wp0xtqrx17
  • Process Group: SingleCell

Overview

This process prepares spatial genomics datasets for analysis by extracting and organizing data from various input formats. It handles both directory-based datasets and compressed archives, automatically detecting the input type and performing appropriate extraction or copying operations. The process is designed to work with spatial transcriptomics data, particularly from platforms like Xenium, by standardizing the data structure for downstream single-cell analysis workflows.

This process is implemented in Bash.

Key Functionality

  • Data Extraction: Automatically detects and extracts data from ZIP archives or copies directory contents
  • Directory Structure Optimization: Flattens nested directory structures to ensure data files are at the appropriate level
  • Format Validation: Verifies input formats and provides error handling for unsupported file types
  • Data Organization: Creates standardized output directory structure for consistent downstream processing

Input/Output Specification

Inputs

Required Inputs

  • Samplesheet
    • Description: Sample metadata file containing information about spatial datasets to be processed
    • Format: Samplesheet format

Outputs

  • Output Directory
    • Description: Organized directory containing extracted and structured spatial genomics data ready for analysis
    • Format: Directory structure

References & Resources

  • Tool Documentation: This process uses standard Unix utilities for file operations and data extraction