Supported tags and respective Dockerfile links

• 2.20

What is bcl2fastq?

The Illumina bcl2fastq2 Conversion Software demultiplexes sequencing data and converts base call (BCL) files into FASTQ files. For more information, please see the latest software guide.

This image is built based on Alpine Linux. It's very lightweight with only 36M in size.

How to use this image

In the following examples, the -d option of the docker run command will run container in background. Please use docker logs -f <container name> to fetch the container log.

Demultiplex to the same run folder

$ docker run -d -v <runfolder-dir>:/mnt/run zymoresearch/bcl2fastq --runfolder-dir /mnt/run

Replace <runfolder-dir> with the real run folder directory on the host machine.

Demultiplex to a different location

This is useful when FASTQ files need to be demultiplexed and stored separately e.g. in a NAS storage device.

$ docker run -d -v <runfolder-dir>:/mnt/run -v <output-dir>:/mnt/output zymoresearch/bcl2fastq \
      --runfolder-dir /mnt/run --output-dir /mnt/output

Replace <runfolder-dir> and <output-dir> with the corresponding directories on the host machine.