Split modalities

A pipeline to split a multimodal mudata files into several unimodal mudata files.

Info

ID: split_modalities
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 1.0.1 -latest \
  -main-script target/nextflow/workflows/multiomics/split_modalities/main.nf \
  --help

Run command

Example of params.yaml

# Inputs
id: # please fill in - example: "foo"
input: # please fill in - example: "input.h5mu"

# Outputs
# output: "$id.$key.output.output"
# output_types: "$id.$key.output_types.csv"

# 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/workflows/multiomics/split_modalities/main.nf \
  -params-file params.yaml

Note

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

Argument groups

Inputs

Name	Description	Attributes
--id	ID of the sample.	string, required, example: "foo"
--input	Path to the sample.	file, required, example: "input.h5mu"

Outputs

Name	Description	Attributes
--output	Output directory containing multiple h5mu files.	file, required, example: "/path/to/output"
--output_types	A csv containing the base filename and modality type per output file.	file, required, example: "types.csv"

Authors

• Dries Schaumont (author, maintainer)

Visualisation

flowchart TB
    v0(Channel.fromList)
    v2(filter)
    v18(split_modalities_component)
    v51(Output)
    v0-->v2
    v2-->v18
    v18-->v51
    style v0 fill:#e3dcea,stroke:#7a4baa;
    style v2 fill:#e3dcea,stroke:#7a4baa;
    style v18 fill:#e3dcea,stroke:#7a4baa;
    style v51 fill:#e3dcea,stroke:#7a4baa;