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nf-core_modules/modules/cellranger/mkfastq
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Regina Hertfelder Reynolds 1b24005f07
Add bcl2fastq2 to cellranger dockerfile (#1115) 
* refactor: add bcl2fastq to cellranger dockerfile

bcl2fastq required for the cellranger mkfastq module and was therefore
added to the cellranger dockerfile. Further, cellranger was updated to
the latest version, 6.1.2., with naming and containers across
cellranger modules updated accordingly.

* chore: add bcl2fastq zip to .gitignore

* style: fix code linting error

* test(cellranger): Add tiles to mkfastq

* additional dockerfile for mkfastq

* update readme and dockerfiles

* update readme

* fix: update container for mkfastq

* docs: correct typos in readme

* test: update md5sum following cellranger update

* test: update md5sum following cellranger update

* fix: new line for external args in mkfastq

* test: update mkfastq tiles argument

* test: comment out mkfastq tests until smaller test data found

* test: stub-run mkfastq test until smaller test data found

* test: fix incorrect file path for mkfastq

Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
2022-01-25 19:58:22 +01:00
..
Dockerfile Add bcl2fastq2 to cellranger dockerfile (#1115) 2022-01-25 19:58:22 +01:00
main.nf Add bcl2fastq2 to cellranger dockerfile (#1115) 2022-01-25 19:58:22 +01:00
meta.yml Add Cell Ranger mkfastq, mkgtf, and count (#979) 2021-12-02 14:27:20 +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>