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Multi h5 explorer Specifications

Process Details

  • Name: Multi_h5_explorer
  • Process UUID: yHiSvl5jtCnSXzyiqLlqI0cE0I8iP0
  • Process Group: SingleCell

Overview

This process systematically searches for and collects HDF5 (.h5) files containing filtered feature-barcode matrices from single-cell RNA sequencing experiments. It navigates through directory structures typical of 10x Genomics Cell Ranger output, ensuring all available h5 files are identified and standardized for downstream single-cell analysis workflows.

This process is implemented in Bash.

Key Functionality

  • Directory Structure Navigation: Automatically searches through per_sample_outs directories to locate single-cell data files
  • File Collection and Standardization: Copies and renames filtered feature-barcode matrix h5 files with consistent sample naming conventions
  • Flexible Path Resolution: Handles different Cell Ranger output directory structures, checking both root and count subdirectories
  • Sample Organization: Organizes multiple sample h5 files in a centralized location for batch processing

Input/Output Specification

Inputs

Required Inputs

  • Input Directory
    • Description: Directory containing single-cell RNA sequencing output data, typically from 10x Genomics Cell Ranger pipeline with per_sample_outs subdirectories
    • Format: Directory

Outputs

  • H5 File
    • Description: Collected and renamed HDF5 files containing filtered feature-barcode matrices for single-cell analysis, with standardized sample naming
    • Format: HDF5 (.h5)

Parameters & Settings

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

References & Resources

  • Tool Documentation: This process uses standard Bash commands for file system operations and does not require additional tool documentation