convert/from_cosmx_to_h5mu
Description
Converts the output from NanoString experiment into a MuData objcet.
<dataset_id>_exprMat_file.csv: File containing the counts.<dataset_id>_metadata_file: File containing the spatial coordinates and additional cell-level metadata.<dataset_id>_fov_file.csv: File containing the coordinates of all the fields of view.
In addition to reading the regular Nanostring output, it loads CellComposite and CellLabels directories, if present,
containing the images.
Arguments
Name | Type & Properties | Description |
|---|---|---|
--input -i | file required | Input folder. Must contain the output from a NanoString CosMx run. |
--modality | string | |
--output -o | file output | The output h5mu file. |
--output_compression | string |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
modality: [ "rna" ]
output: "$id.$key.output.h5mu"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline_spatial.git \
-revision v0.6.0 \
-main-script target/nextflow/convert/from_cosmx_to_h5mu/main.nf \
-params-file params.yaml Relationships
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Current component
convert/from_cosmx_to_h5muopenpipeline_spatial v0.6.0
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