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 2.1.1 -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_types: "$id.$key.output_types.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/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)
    v13(filter)
    v18(split_modalities_component)
    v25(cross)
    v35(cross)
    v45(concat)
    v52(cross)
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    v78(cross)
    v82(Output)
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    v13-->v18
    v18-->v25
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    v13-->v35
    v45-->v52
    v2-->v52
    v52-->v59
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    v2-->v71
    v71-->v78
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    v78-->v82
    v2-->v13
    v35-->v45
    v18-->v35
    v45-->v71
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