filter/subset_cosmx

Description

Filters the output from NanoString experiment to keep only a subset of the fields of view.
Expected input folder structure:
path/to/dataset/
├── CellComposite/
├── CellLabels/
├── CellOverlay/
├── CompartmentLabels/
├── <dataset_id>_exprMat_file.csv
├── <dataset_id>_fov_positions_file.csv
├── <dataset_id>_metadata_file.csv
└── <dataset_id>_tx_file.csv

Type

python_script

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
subset_transcripts_file: [ true ]  
subset_polygons_file: [ true ]  
output: "$id.$key.output.cosmx_data_tiny"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline_spatial.git \  
  -revision v0.3.0 \  
  -main-script target/nextflow/filter/subset_cosmx/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input -i	file required	Input folder. Must contain the output from a NanoString CosMx run.
--num_fovs	integer required	Number of fields of views to keep. Will keep only the first <num_fovs> fields of view.
--subset_transcripts_file	boolean	Whether to subset the <dataset_id>_tx_file.csv file.
--subset_polygons_file	boolean	Whether to subset the <dataset_id>_polygons.csv file.
--output -o	file output	The directory where the subset data will be stored.

Name

Type & Properties

--input

-i

file

required

--num_fovs

integer

required

--subset_transcripts_file

boolean

--subset_polygons_file

boolean

--output

-o

file

output