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Cellranger Ref Checker Specifications

Process Details

  • Name: cellranger_ref_checker
  • Process UUID: GUN9E0YnD1hTx9ZgRMWf4gXPOk3md9
  • Process Group: SingleCell

Overview

This process validates the existence and accessibility of Cell Ranger reference transcriptome directories. It serves as a quality control step to ensure that the specified transcriptome reference folder is present and properly formatted before proceeding with single-cell RNA sequencing analysis workflows.

This process is implemented in Bash, which invokes internal path validation functions to verify directory structure and accessibility.

Key Functionality

  • Reference Validation: Verifies that the specified transcriptome reference directory exists and is accessible
  • Path Resolution: Resolves and validates the full path to the transcriptome folder
  • Error Prevention: Prevents downstream analysis failures by catching missing reference files early in the workflow

Input/Output Specification

Inputs

Optional Inputs

  • Reference
    • Description: Cell Ranger compatible transcriptome reference directory containing genome sequences, annotations, and index files
    • Format: Directory

Outputs

  • Reference
    • Description: Validated transcriptome reference directory ready for use in Cell Ranger analysis
    • Format: Directory

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

The transcriptome parameter is configured through the workflow interface to specify the path to the reference directory.

References & Resources

  • Tool Documentation: Contact the team for details on pathChecker