Nextflow pipeline for bcl2fastq

• rikenbit/ramdaq_bcl2fastq is a Nextflow pipeline for converting and demultiplexing the raw data produced by Illumina sequencing machines (BCL files) into FASTQ files.
• This pipeline can be used as a preprocessor for the ramdaq.

Preparing the execution environment

1. Install nextflow (version >=21.04.0 required)

2. Install either Docker, Singularity, or Apptainer for full pipeline reproducibility (see docs)

3. Verify the container image is available

$ docker run --rm biomehub/bcl2fastq2:2.20.0 bcl2fastq --version
bcl2fastq v2.20.0.422
Copyright (c) 2007-2018 Illumina, Inc.

Converting FASTQ files from a BCL file

# Run bcl2fastq via nextflow
nextflow run rikenbit/ramdaq_bcl2fastq -r main -profile <docker/singularity> --run_dir <directory path>

Note: Nextflow caches the pipeline code locally after the first run. If the repository has been updated, use the -latest flag to pull the latest version of the specified branch:

nextflow run rikenbit/ramdaq_bcl2fastq -r main -latest -profile <docker/singularity> --run_dir <directory path>

Required parameters

• -r main
  • Need to specify explicitly the revision of the ramdaq_bcl2fastq
• --run_dir
  • Full path to the sequencer run directory (the top-level directory containing SampleSheet.csv and Data/Intensities/BaseCalls/)
  • ex: /path/to/210101_A00000_0001_XXXXXXXXXX

Other options

• -profile <docker/singularity/apptainer>
  • Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments.
  • We highly recommend the use of Docker, Singularity, or Apptainer containers for full pipeline reproducibility. If -profile is not specified, the pipeline will run locally and expect software to be installed and available on the PATH.
    • -profile docker : A generic configuration profile to be used with Docker
    • -profile singularity : A generic configuration profile to be used with Singularity
    • -profile apptainer : A generic configuration profile to be used with Apptainer
• --lane_splitting
  • Split output FASTQ files by lane (Default: false, i.e. no lane splitting)
  • ex: --lane_splitting true
• --outdir
  • Rename output directory name (Default: results)
  • The fastq files will be output under ${outdir}/${run directory name}/fastq_files/