Cellranger mkfastq

Demultiplex raw sequencing data


ID: cellranger_mkfastq
Namespace: demux

Example commands

You can run the pipeline using nextflow run.

View help

You can use --help as a parameter to get an overview of the possible parameters.

nextflow run openpipelines-bio/openpipeline \
  -r 0.12.6 -latest \
  -main-script target/nextflow/demux/cellranger_mkfastq/main.nf \

Run command

Example of params.yaml
# Arguments
input: # please fill in - example: "/path/to/bcl"
sample_sheet: # please fill in - example: "SampleSheet.csv"
# output: "$id.$key.output.output"
# reports: "$id.$key.reports.reports"

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"
nextflow run openpipelines-bio/openpipeline \
  -r 0.12.6 -latest \
  -profile docker \
  -main-script target/nextflow/demux/cellranger_mkfastq/main.nf \
  -params-file params.yaml

Replace -profile docker with -profile podman or -profile singularity depending on the desired backend.

Argument group


Name Description Attributes
--input Path to the (untarred) BCL files. Expects ‘RunParameters.xml’ at ‘./’. file, required, example: "/path/to/bcl"
--sample_sheet The path to the sample sheet. file, required, example: "SampleSheet.csv"
--output The folder to store the demux results file, required, default: "fastqs", example: "/path/to/output"
--reports Reports directory file, example: "reports_dir"


  • Angela Oliveira Pisco (author)

  • Samuel D’Souza (author)

  • Robrecht Cannoodt (author, maintainer)