====== BCL_convert ======

BCL_convert is a tool for working with data generated by Illumina sequencing instruments. It is //also// the replacement for **bcl2fastq** which is no longer updated or supported by Illumina.

   * For more information: https://emea.support.illumina.com/sequencing/sequencing_software/bcl-convert.html

<WRAP round box important>
**Roadmap for BCL_convert**

Please note that we now //recommend// the use of the replacement [[:advanced:software:bioapps|Bioapps]] container image which includes BCL_convert and many more common bioinformatics tools and avoids the need for careful matching of dependencies between loaded software modules.
</WRAP>

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===== License Restrictions =====

<code>
- The software can only be used "for the purpose of processing and analyzing data generated from an
Illumina genetic sequencing instrument owned and operated solely by (the University)"

- The software is only to be used for research purposes

- The software can only be used with data generated from the Illumina instrument, and not any data
generated from other sources
</code>

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===== Running on Comet =====

Load the module:

<code lang=bash>
$  module load BCL-Convert
</code>

Run the software:

<code lang=bash>
$ bcl-convert -h
bcl-convert Version 4.4.6
Copyright (c) 2014-2025 Illumina, Inc. 

Run BCL Conversion (BCL directory to *.fastq.gz)
  bcl-convert --bcl-input-directory <BCL_ROOT_DIR> --output-directory <PATH> [options]

Options:
  -h [ --help ]                           Print this help message
  -V [ --version ]                        Print the version and exit
  --output-directory arg                  Output BCL directory for BCL conversion (must be specified)
  -f [ --force ]                          Force: allow destination diretory to already exist
  --bcl-input-directory arg               Input BCL directory for BCL conversion (must be specified)
  --sample-sheet arg                      Path to SampleSheet.csv file (default searched for in --bcl-input-directory)
  --bcl-only-lane arg                     Convert only specified lane number (default all lanes)
  --strict-mode arg                       Abort if any files are missing (false by default)
  --first-tile-only arg                   Only convert first tile of input (for testing & debugging)
  --tiles arg                             Process only a subset of tiles by a regular expression
  --exclude-tiles arg                     Exclude set of tiles by a regular expression
  --bcl-sampleproject-subdirectories arg  Output to subdirectories based upon sample sheet 'Sample_Project' column
  --sample-name-column-enabled arg        Use sample sheet 'Sample_Name' column when naming fastq files & 
                                          subdirectories
  --fastq-gzip-compression-level arg      Set fastq output compression level 0-9 (default 1)
  --shared-thread-odirect-output arg      Use linux native asynchronous io (io_submit) for file output (Default=false)
  --bcl-num-parallel-tiles arg            # of tiles to process in parallel (default 1)
  --bcl-num-conversion-threads arg        # of threads for conversion (per tile, default # cpu threads)
  --bcl-num-compression-threads arg       # of threads for fastq.gz output compression (per tile, default # cpu 
                                          threads, or HW+12)
  --bcl-num-decompression-threads arg     # of threads for bcl/cbcl input decompression (per tile, default half # cpu 
                                          threads, or HW+8. Only applies when preloading files)
  --bcl-only-matched-reads arg            For pure BCL conversion, do not output files for 'Undetermined' [unmatched] 
                                          reads (output by default)
  --run-info arg                          Path to RunInfo.xml file (default root of BCL input directory)
  --no-lane-splitting arg                 Do not split FASTQ file by lane (false by default)
  --create-fastq-for-index-reads arg
  --num-unknown-barcodes-reported arg     # of Top Unknown Barcodes to output (1000 by default)
  --bcl-validate-sample-sheet-only arg    Only validate RunInfo.xml & SampleSheet files (produce no FASTQ files)
  --output-legacy-stats arg               Also output stats in legacy (bcl2fastq2) format (false by default)
  --bcl-enable-tile-metrics arg           Output per-tile metrics in addition to aggregate (true by default)
  --bcl-enable-adapter-cycle-metrics arg  Output per-cycle adapter metrics in addition to aggregate (true by default)
  --bcl-enable-detailed-demux-metrics arg Output demux error cycles and transitions (true by default)
  --no-sample-sheet arg                   Enable legacy no-sample-sheet operation (No demux or trimming. No settings 
                                          supported. False by default, not recommended
</code>

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