workflows/ingestion/conversion
Description
A pipeline to convert .mtx, .h5 or .h5ad file formats to .h5mu.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--id | string required | ID of the sample. |
--input -i | file required | Path to the sample to be converted. Possible format options include: - .h5ad - .h5 - .mtx |
--input_type -t | string required | Type of the input file |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output | file output | Name or template for the output files. |
Conversion from h5ad
Name | Type & Properties | Description |
|---|---|---|
--modality | string multiple | Name of the modality where the h5ad is stored in the h5mu object. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
id: "run"
output: "$id.$key.output.h5mu"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \
-revision v4.2.0 \
-main-script target/nextflow/workflows/ingestion/conversion/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
workflows/ingestion/conversionopenpipeline v4.2.0