Split h5mu

Split the samples of a single modality from a .h5mu (multimodal) sample into seperate .h5mu files based on the values of an .obs column of this modality.

Info

ID: split_h5mu
Namespace: dataflow

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 2.1.1 -latest \
  -main-script target/nextflow/dataflow/split_h5mu/main.nf \
  --help

Run command

Example of params.yaml 
# Input & specifications
input: # please fill in - example: "path/to/file"
modality: "rna"
obs_feature: # please fill in - example: "celltype"
drop_obs_nan: false
ensure_unique_filenames: false

# Outputs
# output: "$id.$key.output"
# output_compression: "gzip"
# output_files: "$id.$key.output_files.csv"

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"

# Arguments
nextflow run openpipelines-bio/openpipeline \
  -r 2.1.1 -latest \
  -profile docker \
  -main-script target/nextflow/dataflow/split_h5mu/main.nf \
  -params-file params.yaml
Note

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

Argument groups

Input & specifications

Name Description Attributes
--input Path to a single .h5mu file. file, required
--modality string, default: "rna"
--obs_feature The .obs column to split the mudata on. string, required, example: "celltype"
--drop_obs_nan Whether to drop all .obs columns that contain only nan values after splitting. boolean_true
--ensure_unique_filenames Append number suffixes to ensure unique filenames after sanitizing obs feature values. boolean_true

Outputs

Name Description Attributes
--output Output directory containing multiple h5mu files. file, required, example: "/path/to/output"
--output_compression The compression format to be used on the output h5mu object. string, example: "gzip"
--output_files A csv containing the base filename and obs feature by which it was split. file, required, example: "sample_files.csv"

Authors

  • Dorien Roosen (author, maintainer)