convert/from_spaceranger_to_h5mu
Description
Converts the output bundle from spaceranger into an h5mu file.
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) |
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. |
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 v0.6.0 \
-main-script target/nextflow/convert/from_spaceranger_to_h5mu/main.nf \
-params-file params.yaml Relationships
Used by
1 relationships
Current component
convert/from_spaceranger_to_h5muopenpipeline_spatial v0.6.0
Uses
0 relationships
No component dependencies found.