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nf-core_modules/modules/cellranger
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Matthias Hörtenhuber e745e167c1
Fix formatting in yaml files, add yamllint config (#1279) 
* fix yml formatting

* allow fastq.gz and fq.gz as file input, add meta.yml and test

* fix yaml files

* Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test"

This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4.

* prettier magic!

* fix comments for yamllint

* remove node version number

* fix linting errors

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 11:15:27 +00:00
..
count Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
mkfastq Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
mkgtf Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
mkref Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
.gitignore Add bcl2fastq2 to cellranger dockerfile (#1115) 2022-01-25 19:58:22 +01:00
Dockerfile Add bcl2fastq2 to cellranger dockerfile (#1115) 2022-01-25 19:58:22 +01:00
README.md Add bcl2fastq2 to cellranger dockerfile (#1115) 2022-01-25 19:58:22 +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>