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nf-core_modules/modules/cellranger/mkfastq
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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
..
Dockerfile Add bcl2fastq2 to cellranger dockerfile (#1115) 2022-01-25 19:58:22 +01:00
main.nf Add when: block (#1261) 2022-02-04 09:53:32 +01:00
meta.yml Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
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

Bcl2fastq2 and Cell Ranger 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 versions in the container and pushing the update to Dockerhub needs to be done manually.

  1. Navigate to the appropriate download pages. - bcl2fastq2: 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: 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 bcl2fastq2 and Cell Ranger versions in this line:

    ENV BCL2FASTQ2_VER=<VERSION> \
    CELLRANGER_VER=<VERSION>

  3. Create and test the container:

    docker build . -t nfcore/cellrangermkfastq:<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/cellrangermkfastq:<CELLRANGER_VERSION>