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The Dockerfile and related shell script files to build a docker container,
which can execute BCL2Fastq.


docker run -d --name bcl2fastq -e "cpu_num=<NUMBER OF CPUs>" -v <RUN FOLDER>:/run -v <OUTPUT FOLDER>:/output hunterchung/bcl2fastq-docker


  • <NUMBER OF CPUs>: BCL2Fastq process can be parallelilzed. Use a reasonable number depending
    on the setup of your computer or computing cluster.
  • <RUN FOLDER>: The full path of the run folder. E.g. .
  • OUTPUT FOLDER: The process will create a Unaligned folder inside the OUTPUT FOLDER you specifiy here. The Unaligned contains all Fastq files.


  • If you want to access the container after running (maybe for debugging), do not use --rm=true argument.
  • use docker logs bcl2fastq to access the log files.
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