Conversion

A pipeline to convert different file formats to .h5mu.

Info

ID: conversion
Namespace: workflows/ingestion

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/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"

nextflow run openpipelines-bio/openpipeline \
  -r 1.0.1 -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)
    v19(from_10xh5_to_h5mu)
    v78(mix)
    v42(from_h5ad_to_h5mu)
    v65(from_10xmtx_to_h5mu)
    v94(Output)
    v0-->v2
    v2-->v19
    v19-->v78
    v2-->v42
    v42-->v78
    v2-->v65
    v65-->v78
    v78-->v94
    style v0 fill:#e3dcea,stroke:#7a4baa;
    style v2 fill:#e3dcea,stroke:#7a4baa;
    style v19 fill:#e3dcea,stroke:#7a4baa;
    style v78 fill:#e3dcea,stroke:#7a4baa;
    style v42 fill:#e3dcea,stroke:#7a4baa;
    style v65 fill:#e3dcea,stroke:#7a4baa;
    style v94 fill:#e3dcea,stroke:#7a4baa;