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nf-core_modules/modules/cellranger
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Alexander Peltzer b573ff053e
Bugfix for CellRanger Dockerfile (#1812) 
Bugfix to enable Singularity support
2022-06-27 11:07:33 +02:00
..
count make module output meta map (#1803) 2022-06-23 12:43:06 +02:00
mkfastq Bugfix for CellRanger Dockerfile (#1812) 2022-06-27 11:07:33 +02:00
mkgtf Update main.nf 2022-06-10 10:53:48 +02:00
mkref Update main.nf 2022-06-10 10:54:06 +02:00
.gitignore Add bcl2fastq2 to cellranger dockerfile (#1115) 2022-01-25 19:58:22 +01:00
Dockerfile Update Dockerfile 2022-06-10 10:52:13 +02:00
README.md Prettier (#1405) 2022-03-18 14:27:50 +01:00

README.md

Updating the docker container and making a new module release

Cell Ranger is a commercial tool from 10X Genomics. The container provided for the cellranger nf-core module is not provided nor supported by 10x Genomics. Updating the Cell Ranger versions in the container and pushing the update to Dockerhub needs to be done manually.

  1. Navigate to the appropriate download page. - Cell Ranger: download the tar ball of the desired Cell Ranger version with curl or wget. Place this file in the same folder where the Dockerfile lies.

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

    ENV CELLRANGER_VER=<VERSION>

  3. Create and test the container:

    docker build . -t nfcore/cellranger:<VERSION>

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

    docker push nfcore/cellranger:<VERSION>