convert/from_h5mu_to_seurat
Description
Converts an h5mu file into a Seurat file.
Restrictions:
Only the intersection of cells is currently loaded into the Seurat object due to the object structure limitation.
Multimodal embeddings (global .obsm slot) are loaded with the assay.used field set to the default assay.
Embeddings names are changed in order to comply with R & Seurat requirements and conventions.
Feature names with underscores ('_') are automatically replaced with dashes ('-')
Seurat does not support global variables metadata /var.
Arguments
Name | Type & Properties | Description |
|---|---|---|
--input -i | file required | Input h5mu file |
--output -o | file required output | Output Seurat file |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output: "$id.$key.output.rds"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \
-revision v4.0.3 \
-main-script target/nextflow/convert/from_h5mu_to_seurat/main.nf \
-params-file params.yaml Relationships
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Current component
convert/from_h5mu_to_seuratopenpipeline v4.0.3
Uses
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