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: workflows/multiomics

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 2.1.0 -latest \
  -main-script target/nextflow/workflows/multiomics/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 2.1.0 -latest \
  -profile docker \
  -main-script target/nextflow/workflows/multiomics/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

• Dries Schaumont (author, maintainer)

Visualisation

flowchart TB
    v0(Channel.fromList)
    v2(filter)
    v13(filter)
    v18(split_h5mu_component)
    v25(cross)
    v35(cross)
    v45(concat)
    v52(cross)
    v59(cross)
    v71(cross)
    v78(cross)
    v82(Output)
    v0-->v2
    v13-->v18
    v18-->v25
    v13-->v25
    v13-->v35
    v45-->v52
    v2-->v52
    v52-->v59
    v2-->v59
    v2-->v71
    v71-->v78
    v2-->v78
    v78-->v82
    v2-->v13
    v35-->v45
    v18-->v35
    v45-->v71
    style v0 fill:#e3dcea,stroke:#7a4baa;
    style v2 fill:#e3dcea,stroke:#7a4baa;
    style v13 fill:#e3dcea,stroke:#7a4baa;
    style v18 fill:#e3dcea,stroke:#7a4baa;
    style v25 fill:#e3dcea,stroke:#7a4baa;
    style v35 fill:#e3dcea,stroke:#7a4baa;
    style v45 fill:#e3dcea,stroke:#7a4baa;
    style v52 fill:#e3dcea,stroke:#7a4baa;
    style v59 fill:#e3dcea,stroke:#7a4baa;
    style v71 fill:#e3dcea,stroke:#7a4baa;
    style v78 fill:#e3dcea,stroke:#7a4baa;
    style v82 fill:#e3dcea,stroke:#7a4baa;