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

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

3. Build a Docker image for bcl2fastq with the following command

docker build -t bcl2fastq2:1.0 github.com/rikenbit/ramdaq_bcl2fastq#main

4. Run test

$ docker run --rm bcl2fastq2:1.0 bcl2fastq --help
BCL to FASTQ file converter
bcl2fastq v2.17.1.14
Copyright (c) 2007-2015 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>

Required parameters

• -r main
  • Need to specify explicitly the revision of the ramdaq_bcl2fastq
• --run_dir
  • Requires a BaseCalls directory path(full) containing the binary base call files (BCL files)
  • ex: ${required directory path}/Data/Intensities/BaseCalls

Other options

• -profile <docker/singularity>
  • Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments.
  • We highly recommend the use of Docker or Singularity 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
• --lane_splitting
  • If this option is specified, output fastq files are split by lane
• --outdir
  • Rename output directory name (Default : results)
  • The fastq files will be output under "${outdir}/${run directory name}/fastq_files/"