Conversion
A pipeline to convert different file formats to .h5mu.
Info
ID: conversion
Namespace: ingestion
Links
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: ":" |
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