Description
Creates a SpatialExperiment object from the downloaded unzipped CosMx directory for Nanostring
CosMx spatial gene expression data, and saves it as a SpatialExperiment object.
The constructor assumes the downloaded unzipped CosMx Folder has the following structure:
Mandatory files
· | — *_exprMat_file.csv
· | — *_metadata_file.csv
Optional files, by default added to the metadata() as a list of paths (will be converted to parquet):
· | —*_fov_positions_file.csv
· | — *_tx_file.csv
· | — *_polygons.csv
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
add_tx_path: [ true ]
add_polygon_path: [ true ]
add_fov_positions: [ true ]
alternative_experiment_features: [ "NegPrb", "Negative", "SystemControl", "FalseCode" ]
output: "$id.$key.output.rds"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline_spatial.git \
-revision v0.1.0 \
-main-script target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf \
-params-file params.yaml Name | Type & Properties |
|---|---|
--input -i | file required |
--add_tx_path | boolean |
--add_polygon_path | boolean |
--add_fov_positions | boolean |
--alternative_experiment_features | string multiple |
--output -o | file required output |