convert/from_10xh5_to_h5mu
Description
Converts a 10x h5 into an h5mu file.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input -i | file required | A 10x h5 file as generated by Cell Ranger. |
--input_metrics_summary | file | A metrics summary csv file as generated by Cell Ranger. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output -o | file output | Output h5mu file. |
--uns_metrics | string | Name of the .uns slot under which to QC metrics (if any). |
--output_compression | string | Compression format to use for the output AnnData and/or Mudata H5 files. By default no compression is applied. |
Arguments
Name | Type & Properties | Description |
|---|---|---|
--min_genes | integer | Minimum number of counts required for a cell to pass filtering. |
--min_counts | integer | Minimum number of genes expressed required for a cell to pass filtering. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output: "$id.$key.output.h5mu"
uns_metrics: [ "metrics_cellranger" ]
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \
-revision v4.2.0 \
-main-script target/nextflow/convert/from_10xh5_to_h5mu/main.nf \
-params-file params.yaml Relationships
Used by
2 relationships
Current component
convert/from_10xh5_to_h5muopenpipeline v4.2.0
Uses
0 relationships
No component dependencies found.