Conversion

A pipeline to convert different file formats to .h5mu.

Info

ID: conversion
Namespace: 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 0.12.0 -latest \
  -main-script ./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 0.12.0 -latest \
  -profile docker \
  -main-script ./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.	List of file, required, example: "input.h5mu", multiple_sep: ";"
--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 LR
    v0(Input)
    v2(toSortedList)
    v4(flatMap)
    v5(filter)
    v10(from_10xh5_to_h5mu)
    v12(join)
    v35(mix)
    v15(filter)
    v20(from_10xmtx_to_h5mu)
    v22(join)
    v25(filter)
    v30(from_h5ad_to_h5mu)
    v32(join)
    v37(toSortedList)
    v39(Output)
    v4-->v5
    v4-->v15
    v4-->v25
    v0-->v2
    v2-->v4
    v5-->v12
    v5-->v10
    v10-->v12
    v12-->v35
    v15-->v22
    v15-->v20
    v20-->v22
    v22-->v35
    v25-->v32
    v25-->v30
    v30-->v32
    v32-->v35
    v35-->v37
    v37-->v39