Cellranger count split

Split 10x Cell Ranger output directory into separate output fields.


ID: cellranger_count_split
Namespace: mapping

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 1.0.1 -latest \
  -main-script target/nextflow/mapping/cellranger_count_split/main.nf \

Run command

Example of params.yaml
# Arguments
input: # please fill in - example: "input_dir"
# filtered_h5: "$id.$key.filtered_h5.h5"
# metrics_summary: "$id.$key.metrics_summary.csv"
# molecule_info: "$id.$key.molecule_info.h5"
# bam: "$id.$key.bam.bam"
# bai: "$id.$key.bai.bai"
# raw_h5: "$id.$key.raw_h5.h5"

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"
nextflow run openpipelines-bio/openpipeline \
  -r 1.0.1 -latest \
  -profile docker \
  -main-script target/nextflow/mapping/cellranger_count_split/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 Output directory from a Cell Ranger count run. file, required, example: "input_dir"
--filtered_h5 file, example: "filtered_feature_bc_matrix.h5"
--metrics_summary file, example: "metrics_summary.csv"
--molecule_info file, example: "molecule_info.h5"
--bam file, example: "possorted_genome_bam.bam"
--bai file, example: "possorted_genome_bam.bam.bai"
--raw_h5 file, example: "raw_feature_bc_matrix.h5"


  • Angela Oliveira Pisco (author)

  • Samuel D’Souza (author)

  • Robrecht Cannoodt (author, maintainer)