convert/from_spaceranger_to_h5mu

Description

Converts the output bundle from spaceranger into an h5mu file.

Type

python_script

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.h5mu"  
modality: [ "rna" ]  
uns_metrics: [ "metrics_spaceranger" ]  
uns_probe_set: [ "probe_set" ]  
obsm_coordinates: [ "spatial" ]  
output_type: [ "filtered" ]  
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/convert/from_spaceranger_to_h5mu/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required	Convert spatial data resulting from Aviti Teton sequencers that have been processed by the Element Biosciences cells2stats workflow to H5MU format. This component processes cells2stats count matrices to create a standardized H5MU file for downstream analysis. The component reads: - Parquet file containing the count matrix and metadata - Panel.json with target and batch information And outputs an H5MU file with: - Count data as the main .X matrix - Spatial coordinates in obsm - Cell Paint intensities in obsm (optional) - Nuclear count data as a layer (optional) - CellProfiler morphology metrics in obsm (optional) - Unassigned targets in obsm (optional)

Name

Type & Properties

--input

-i

file

required

Outputs

Name	Type & Properties	Description
--output	file output	Output h5mu file.
--modality	string	Name of the modality under which to store the data.
--uns_metrics	string	Name of the .uns slot under which to QC metrics (if any).
--uns_probe_set	string	Name of the .uns slot under which to store probe set information (if any).
--obsm_coordinates	string	Name of the .obsm slot under which to store the cell centroid coordinates.
--output_type	string	Which Spaceranger output to use for converting to h5mu.
--output_compression	string	Compression to use when writing the h5mu file.

Name

Type & Properties

--output

file

output

--modality

string

--uns_metrics

string

--uns_probe_set

string

--obsm_coordinates

string

--output_type

string

--output_compression

string