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Bcl Convert Specifications

Process Details

  • Name: bclConvert
  • Process UUID: bu5eoHncdaBIAaJQRT8W0lveiWhaiU
  • Process Group: SingleCell

Overview

This process converts Illumina BCL (Base Call) files to FASTQ format using Illumina's bcl-convert tool. It is designed for single-cell sequencing workflows where raw sequencer output needs to be demultiplexed and converted to standard FASTQ files. The process organizes output files by creating dedicated directories for FASTQ files and reports, and copies essential HTML reports to accessible locations for quality assessment.

This process is implemented in Bash, utilizing Illumina's bcl-convert tool within a containerized environment.

Key Functionality

  • BCL to FASTQ Conversion: Converts raw Illumina BCL files to standard FASTQ format using bcl-convert
  • File Organization: Automatically organizes output into separate directories for FASTQ files and reports
  • Report Management: Moves Reports and Logs to a dedicated reports directory and copies key HTML files for easy access
  • Sample Sheet Integration: Supports custom sample sheets for demultiplexing configuration

Input/Output Specification

Inputs

Required Inputs

  • BCL Files
    • Description: Raw Illumina sequencer output files containing base call data
    • Format: BCL file set

Outputs

  • Reads

    • Description: Demultiplexed sequencing reads in standard format
    • Format: FASTQ

  • Output Directory

    • Description: Organized directory structure containing processed FASTQ files and associated reports
    • Format: Directory

Parameters & Settings

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

  • Bclconvert Parameters
    • Description: Optional bclconvert parameters
    • Default value: "" (empty)

References & Resources

  • Tool Documentation: Contact the team for details on bcl-convert usage and configuration options