# Updating the docker container and making a new module release

Bcl2fastq2 and Cell Ranger ATAC are commercial tools from Illumina and 10X Genomics, respectively. The container
provided for the cellranger nf-core module is not provided nor supported by either Illumina or 10x Genomics. Updating
the bcl2fastq2 or Cell Ranger ATAC versions in the container and pushing the update to Dockerhub needs to be done manually.

1. Navigate to the appropriate download pages. - [bcl2fastq2](https://emea.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html): download the linux rpm installer of the desired bcl2fastq2 version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies. - [Cell Ranger ATAC](https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/installation): download the tar ball of the desired Cell Ranger ATAC version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.

2. Edit the Dockerfile. Update the bcl2fastq2 and Cell Ranger versions in this line:

   ```bash
   ENV BCL2FASTQ2_VER=<VERSION> \
       CELLRANGERATAC_VER=<VERSION>
   ```

3. Create and test the container:

   ```bash
   docker build . -t quay.io/nf-core/cellranger-atac-mkfastq:<CELLRANGERATAC_VERSION>
   ```

4. Access rights are needed to push the container to the Dockerhub nfcore organization, please ask a core team
   member to do so.

   ```bash
   docker push quay.io/nf-core/cellranger-atac-mkfastq:<CELLRANGERATAC_VERSION>
   ```
