hunterchung/bcl2fastq-docker repository overview

⁠bcl2fatq-docker

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

⁠Qickstart

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

⁠Variables

• <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.

⁠Troubleshooting

• 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.