From cellranger multi to h5mu

Converts the output from cellranger multi to a single .h5mu file.


ID: from_cellranger_multi_to_h5mu
Namespace: convert

By default, will map the following library type names to modality names: - Gene Expression: rna - Peaks: atac - Antibody Capture: prot - VDJ: vdj - VDJ-T: vdj_t - VDJ-B: vdj_b - CRISPR Guide Capture: crispr - Multiplexing Capture: hashing

Other library types have their whitepace removed and dashes replaced by underscores to generate the modality name.

Currently does not allow parsing the output from cell barcode demultiplexing.

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/convert/from_cellranger_multi_to_h5mu/ \

Run command

Example of params.yaml
# Arguments
input: # please fill in - example: "input_dir_containing_modalities"
# output: "$id.$key.output.h5mu"
# output_compression: "gzip"
uns_metrics: "metrics_cellranger"

# 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/convert/from_cellranger_multi_to_h5mu/ \
  -params-file params.yaml

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

Argument group


Name Description Attributes
--input Input folder. Must contain the output from a cellranger multi run. file, required, example: "input_dir_containing_modalities"
--output Output h5mu file. file, example: "output.h5mu"
--output_compression string, example: "gzip"
--uns_metrics Name of the .uns slot under which to QC metrics (if any). string, default: "metrics_cellranger"


  • Dries Schaumont (maintainer)