ingestion_qc/detect_ingestion_method
Description
Detects the ingestion method of a dataset.
Currently detects either 10X CellRanger Multi, 10X Xenium or Nanostring CosMx, but can be extended to other technologies upon request.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input | file required | The input h5mu file(s) |
--modality | string | The modality to use |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output_uns_ingestion_method | string | The .uns field in which to store the exprimental setup. Values stored are `cellranger_multi`, `xenium` or `cosmx`. |
--output | file required output | The output h5mu file, containing an .uns field with experiment description. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
modality: [ "rna" ]
output_uns_ingestion_method: [ "ingestion_method" ]
output: "$id.$key.output.h5mu"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline_qc.git \
-revision v0.2.1 \
-main-script target/nextflow/ingestion_qc/detect_ingestion_method/main.nf \
-params-file params.yaml Relationships
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Current component
ingestion_qc/detect_ingestion_methodopenpipeline_qc v0.2.1
Uses
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