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Cellranger Multi Libraries Prep Specifications

Process Details

  • Name: cellranger_multi_libraries_prep
  • Process UUID: c663ziiq46j6ax6952g5sf6b3b4z3e
  • Process Group: SingleCell

Overview

This process prepares for the execution of the "cellranger multi" command by grouping configuration files based on the provided libraries. It organizes library metadata and configuration settings to enable proper execution of Cell Ranger Multi workflows for single-cell RNA sequencing data processing.

This process is implemented in Groovy.

Key Functionality

  • Library Organization: Groups and organizes FASTQ files based on user-defined criteria
  • Configuration Preparation: Generates library settings configuration for Cell Ranger Multi execution
  • Feature Type Assignment: Associates appropriate feature types with each library for multi-modal analysis
  • Group-based Processing: Enables separate processing of different library groups in individual jobs

Input/Output Specification

Inputs

This process does not require file inputs but uses configurable parameters to generate library settings.

Outputs

  • librarySettings
    • Description: Configuration object containing organized library metadata including FASTQ identifiers, group assignments, and feature types for Cell Ranger Multi processing
    • Format: librarySettings object

Parameters & Settings

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

  • Libraries

    • Description: A name to identify fastq file
    • Default value: (user-defined)

  • Group

    • Description: Optional. Use this column to run Cell Ranger Multi separately for different groups of files. Files that share the same group value will be grouped together and processed in individual jobs
    • Default value: (user-defined)

  • Feature Types

    • Description: Type of features contained in the library
    • Available options: Gene Expression (default), Antibody Capture, CRISPR Guide Capture, Multiplexing Capture, VDJ, VDJ-T, VDJ-T-GD, VDJ-B, Antigen Capture, Custom

References & Resources

  • Tool Documentation: Contact the team for details on Cell Ranger Multi configuration
  • Related Papers: Zheng, G.X.Y., Terry, J.M., Belgrader, P. et al. Massively parallel digital transcriptional profiling of single cells. Nat Commun 8, 14049 (2017). https://doi.org/10.1038/ncomms14049