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nf-core_modules/modules/cellranger
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Edmund Miller e2ba70ed9a
Add Cell Ranger mkfastq, mkgtf, and count (#979) 
* feat(cellranger): Add initial count module

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>

* feat(cellranger): Add mkgtf module

* test(cellranger): Fix count test with mkgtf

* fix(cellranger): Generalize gtf attribute filters

* chore: Add .gitignore for cellranger tar

* build(cellranger): Update dockerfile

https://joshtronic.com/2021/09/12/fixed-repository-debian-security-buster-updates-changed-suite-from-stable-to-oldstable/

* Apply suggestions from code review

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update modules/cellranger/mkgtf/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* style: Capitalize README

* test(cellranger): Update pytest_modules

* feat(cellranger): Add initial mkfastq module

* ci: Update pytest modules

* refactor(cellranger): Update modules to new syntax

* docs(cellranger): Update meta files

There is some terrible copy-pasting going on.

* fix(cellranger): Add args

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-12-02 14:27:20 +00:00
..
count Add Cell Ranger mkfastq, mkgtf, and count (#979) 2021-12-02 14:27:20 +00:00
mkfastq Add Cell Ranger mkfastq, mkgtf, and count (#979) 2021-12-02 14:27:20 +00:00
mkgtf Add Cell Ranger mkfastq, mkgtf, and count (#979) 2021-12-02 14:27:20 +00:00
mkref Add Cell Ranger mkfastq, mkgtf, and count (#979) 2021-12-02 14:27:20 +00:00
.gitignore Add Cell Ranger mkfastq, mkgtf, and count (#979) 2021-12-02 14:27:20 +00:00
Dockerfile Add Cell Ranger mkfastq, mkgtf, and count (#979) 2021-12-02 14:27:20 +00:00
README.md Add Cell Ranger mkfastq, mkgtf, and count (#979) 2021-12-02 14:27:20 +00:00

README.md

Updating the docker container and making a new module release

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

  1. Navigate to the Cell Ranger download page and 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 version in this line:

    ENV CELLRANGER_VER <VERSION>

  3. Create the container:

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