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.
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 v0.1.1 \
-main-script target/nextflow/convert/from_cosmx_to_h5mu/main.nf \
-params-file params.yaml Name | Type & Properties |
|---|---|
--input -i | file required |
--modality | string |
--output -o | file output |
--output_compression | string |