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Demultiplexer Prep Specifications

Process Details

  • Name: demultiplexer_prep
  • Process UUID: txiamXE2YTGUZHyJiwust9jHB0lhXV
  • Process Group: SingleCell

Overview

This process prepares the BCL directory and SampleSheet.csv file for the "mkfastq" process in single-cell RNA sequencing workflows. It creates symbolic links or copies the necessary files based on the inputs provided, ensuring proper organization of sequencing data before demultiplexing.

This process is implemented in Groovy/Nextflow, which handles file preparation and organization tasks for BCL Convert processing.

Key Functionality

  • BCL Directory Preparation: Organizes and prepares the BCL directory structure for downstream demultiplexing
  • Sample Sheet Validation: Processes and validates the SampleSheet.csv file required for BCL Convert
  • File Organization: Creates appropriate symbolic links or copies files to ensure proper data structure for the mkfastq process

Input/Output Specification

Inputs

This process uses configurable parameters rather than traditional file inputs.

Outputs

  • bcl

    • Description: Prepared BCL data structure ready for demultiplexing
    • Format: BCL format

  • bcl_directory

    • Description: Organized BCL directory containing all necessary files for the mkfastq process
    • Format: BCL directory structure

Parameters & Settings

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

  • BCL Directory Location

    • Description: Location of bcl directory. e.g. s3://bio/BCLfolder/
    • Default value: (empty string)

  • Sample Sheet Path

    • Description: The SampleSheet.csv file path. By default, this file should be located in the BCL directory. If it's missing from that directory or you need to specify a different location, please provide the full path to the file. For example: s3://bio/BCLfolder/SampleSheet2.csv
    • Default value: (empty string)

References & Resources

  • Tool Documentation: BCL Convert Sample Sheet Documentation
  • Related Papers: Van der Auwera, G.A. & O'Connor, B.D. (2020). Genomics in the Cloud: Using Docker, GATK, and WDL in Terra. O'Reilly Media.