Cellranger mkfastq

Demultiplex raw sequencing data

Info

ID: cellranger_mkfastq
Namespace: demux

Links

Source

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 1.0.2 -latest \
  -main-script target/nextflow/demux/cellranger_mkfastq/main.nf \
  --help

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 1.0.2 -latest \
  -profile docker \
  -main-script target/nextflow/demux/cellranger_mkfastq/main.nf \
  -params-file params.yaml

Note

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

Argument group

Arguments

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"

Authors

• Angela Oliveira Pisco (author)

• Samuel D’Souza (author)

• Robrecht Cannoodt (author, maintainer)