convert/velocyto_to_h5mu
Description
Convert a velocyto loom file to a h5mu file.
If an input h5mu file is also provided, the velocity
h5ad object will get added to that h5mu instead.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input_loom | file required | Path to the input loom file. |
--input_h5mu | file | If a MuData file is provided, |
--modality | string | The name of the modality to operate on. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output | file output | Path to the output MuData file. |
--layer_spliced | string | Output layer for the spliced reads. |
--layer_unspliced | string | Output layer for the unspliced reads. |
--layer_ambiguous | string | Output layer for the ambiguous reads. |
--output_compression | string | Compression format to use for the output AnnData and/or Mudata objects. By default no compression is applied. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
modality: [ "rna_velocity" ]
output: "$id.$key.output.h5mu"
layer_spliced: [ "velo_spliced" ]
layer_unspliced: [ "velo_unspliced" ]
layer_ambiguous: [ "velo_ambiguous" ]
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \
-revision v3.0.2 \
-main-script target/nextflow/convert/velocyto_to_h5mu/main.nf \
-params-file params.yaml Relationships
Used by
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No components use this component.
Current component
convert/velocyto_to_h5muopenpipeline v3.0.2
Uses
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