Convert to MuData

A pipeline to convert different file formats to .h5mu.

Info

ID: conversion
Namespace: workflows/ingestion

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/ingestion/conversion/main.nf \
  --help

Run command

Example of params.yaml 
# Inputs
id: # please fill in - example: "foo"
input: # please fill in - example: "input.h5mu"
input_type: # please fill in - example: "foo"

# Outputs
# output: "$id.$key.output.h5mu"

# Conversion from h5ad
# modality: ["foo"]

# 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/ingestion/conversion/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"
--input_type Type of the input file string, required

Outputs

Name Description Attributes
--output Name or template for the output files. file, example: "output.h5mu"

Conversion from h5ad

Name Description Attributes
--modality Name of the modality where the h5ad is stored in the h5mu object. List of string, multiple_sep: ";"

Authors

  • Dries Schaumont (author, maintainer)

  • Dries De Maeyer (author)

Visualisation

flowchart TB
    v0(Channel.fromList)
    v2(filter)
    v12(filter)
    v20(from_10xh5_to_h5mu)
    v27(cross)
    v37(cross)
    v117(mix)
    v48(filter)
    v56(from_h5ad_to_h5mu)
    v63(cross)
    v73(cross)
    v84(filter)
    v92(from_10xmtx_to_h5mu)
    v99(cross)
    v109(cross)
    v124(cross)
    v131(cross)
    v143(cross)
    v150(cross)
    v154(Output)
    v0-->v2
    v12-->v20
    v20-->v27
    v12-->v27
    v12-->v37
    v48-->v56
    v56-->v63
    v48-->v63
    v48-->v73
    v84-->v92
    v92-->v99
    v84-->v99
    v84-->v109
    v117-->v124
    v2-->v124
    v124-->v131
    v2-->v131
    v2-->v143
    v143-->v150
    v2-->v150
    v150-->v154
    v2-->v12
    v37-->v117
    v20-->v37
    v2-->v48
    v73-->v117
    v56-->v73
    v2-->v84
    v109-->v117
    v92-->v109
    v117-->v143
    style v0 fill:#e3dcea,stroke:#7a4baa;
    style v2 fill:#e3dcea,stroke:#7a4baa;
    style v12 fill:#e3dcea,stroke:#7a4baa;
    style v20 fill:#e3dcea,stroke:#7a4baa;
    style v27 fill:#e3dcea,stroke:#7a4baa;
    style v37 fill:#e3dcea,stroke:#7a4baa;
    style v117 fill:#e3dcea,stroke:#7a4baa;
    style v48 fill:#e3dcea,stroke:#7a4baa;
    style v56 fill:#e3dcea,stroke:#7a4baa;
    style v63 fill:#e3dcea,stroke:#7a4baa;
    style v73 fill:#e3dcea,stroke:#7a4baa;
    style v84 fill:#e3dcea,stroke:#7a4baa;
    style v92 fill:#e3dcea,stroke:#7a4baa;
    style v99 fill:#e3dcea,stroke:#7a4baa;
    style v109 fill:#e3dcea,stroke:#7a4baa;
    style v124 fill:#e3dcea,stroke:#7a4baa;
    style v131 fill:#e3dcea,stroke:#7a4baa;
    style v143 fill:#e3dcea,stroke:#7a4baa;
    style v150 fill:#e3dcea,stroke:#7a4baa;
    style v154 fill:#e3dcea,stroke:#7a4baa;