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nf-core_modules/modules/cellranger
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James A. Fellows Yates a0443e2c54
Fixes incorrectly quoted tags (#2113) 
* Update main.nf

* Update meta.yml

* Re-add logos as not staged in a way that works with MultiQC config files

* Update main.nf

* Remove now unnecessary input channel

* Remove unused channel from tests

* Update hAMRonization to 1.1.1 and add hAMRonization farGene

* Fix hamronizatio ntests

* Prettier

* Fix fargene linting

* Correct file

* Fix fargene output

* Apply suggestions from code review

Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>

* Fix summarise tests

* Prettier

* Fix incorrect quotes in tags

Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
 		2 years ago
..
count make module output meta map (#1803) 2 years ago
mkfastq Bugfix for CellRanger Dockerfile (#1812) 2 years ago
mkgtf Update main.nf 2 years ago
mkref Fixes incorrectly quoted tags (#2113) 2 years ago
.gitignore Add bcl2fastq2 to cellranger dockerfile (#1115) 2 years ago
Dockerfile Update Dockerfile 2 years ago
README.md Prettier (#1405) 2 years ago

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>