nf-core/cellranger/mkfastq @ 0.0.0-3fc6d40

Module to create FASTQs needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkfastq command.

reference mkfastq fastq illumina bcl2fastq

Latest version: 0.0.0-3fc6d40

Total downloads: 6

Source: nf-core/modules

Authors: @ggabernet @edmundmiller @RHReynolds

Maintainers: @ggabernet @edmundmiller @RHReynolds

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.

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.
Edit the Dockerfile. Update the bcl2fastq2 and Cell Ranger versions in this line:

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

Create and test the container:

docker build -f Dockerfile.manual -t quay.io/nf-core/cellrangermkfastq:<CELLRANGER_VERSION> .

Access rights are needed to push the container to the Dockerhub nfcore organization, please ask a core team member to do so.

docker push quay.io/nf-core/cellrangermkfastq:<CELLRANGER_VERSION>

Process

`Name`	`CELLRANGER_MKFASTQ`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`csv` file	Sample sheet `*.csv`
`bcl` file	Base call files `*.bcl.bgzf`

Output 7 channels

#1 fastq tuple

`meta` map	Groovy Map containing sample information
`_outs/outs/fastq_path//_S[0-9]_R?_00?.fastq.gz` file	Read FastQ files `_S[0-9]_R?_00?.fastq.gz`

#2 stats tuple

`meta` map	Groovy Map containing sample information
`*_outs/outs/fastq_path/Stats` directory	Stats `Stats`

#3 interop tuple

`meta` map	Groovy Map containing sample information
`_outs/outs/interop_path/.bin` file	InterOp files `*.bin`

#4 reports tuple

`meta` map	Groovy Map containing sample information
`*_outs/outs/fastq_path/Reports` directory	Reports `Reports`

#5 fastq_idx tuple

`meta` map	Groovy Map containing sample information
`_outs/outs/fastq_path//_S[0-9]_I?_00?.fastq.gz` file	Index FastQ files `_S[0-9]_I?_00?.fastq.gz`

#6 undetermined_fastq tuple

`meta` map	Groovy Map containing sample information
`_outs/outs/fastq_path/Undetermined.fastq.gz` file	Undetermined FastQ files `Undetermined*.fastq.gz`

#7 versions_cellranger tuple

`${task.process}` string	The name of the process
`cellranger` string	The name of the tool
`cellranger --version \| sed "s/.*-//"` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
cellranger	Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.	https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger

Version	0.0.0-3fc6d40
Commit ID	3fc6d40d163d89ae44d40a00b9017d5a9df5170e
Release Date	22 Apr 2026 15:05:22 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fcellranger%2Fmkfastq/0.0.0-3fc6d40/download