Workflows such as cellranger_workflow and dropseq_workflow provide the option of running bcl2fastq. We provide dockers containing bcl2fastq that are accessible only by members of the Broad Institute. Non-Broad Institute members will have to provide their own docker images. Please note that if you’re a Broad Institute member and are not able to pull the docker image, please check https://app.terra.bio/#groups to see that you’re a member of the all_broad_users group. If not, please contact Terra support and ask to be added to the all_broad_users@firecloud.org group.


Read this tutorial if you are new to Docker.

Then for a Debian based docker (e.g. continuumio/miniconda3), create the Dockerfile as follows:

RUN apt-get update && apt-get install --no-install-recommends -y alien unzip
ADD bcl2fastq2-v2-20-0-linux-x86-64.zip /software/
RUN unzip -d /software/ /software/bcl2fastq2-v2-20-0-linux-x86-64.zip && alien -i /software/bcl2fastq2-v2.20.0.422-Linux-x86_64.rpm && rm /software/bcl2fastq2-v2*

Next, download bcl2fastq from the Illumina website, which requires registration. Choose the Linux rpm file format and download bcl2fastq2-v2-20-0-linux-x86-64.zip to the same directory as your Dockerfile.

You can host your private docker images in the Google Container Registry.


In this example we create a docker image for running cellranger mkfastq version 3.0.2.

  1. Create a GCP project or reuse an existing project.

  2. Enable the Google Container Registry

  3. Clone the cumulus repository:

    git clone https://github.com/lilab-bcb/cumulus.git
  4. Add the lines to cumulus/docker/cellranger/3.0.2/Dockerfile to include bcl2fastq (see Docker).

  5. Ensure you have Docker installed

  6. Download cellranger from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/3.0

  7. Build, tag, and push the docker. Remember to replace PROJECT_ID with your GCP project id:

    cd cumulus/docker/cellranger/3.0.2/
    docker build -t cellranger-3.0.2 .
    docker tag cellranger-3.0.2 gcr.io/PROJECT_ID/cellranger:3.0.2
  8. Import cellranger_workflow workflow to your workspace (see cellranger_workflow steps), and enter your docker registry URL (in this example, "gcr.io/PROJECT_ID/") in cellranger_mkfastq_docker_registry field of cellranger_workflow inputs.