preprocessing/calculate_qc_metrics
Description
Calculate quality control metrics.
Computes a number of per-cell (.obs) and per-gene (.var) quality control
metrics from a count matrix, such as the number of genes per cell, the
total counts per cell, the number of cells per gene, and the percentage
of counts dropped out per gene.
Wraps rapids_singlecell.pp.calculate_qc_metrics.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input -i | file required | Input h5mu file. |
--modality | string | Which modality from the input MuData file to process. |
--layer | string | Layer to compute QC metrics from. By default, X is used. |
--qc_vars | string multiple | Names of boolean columns in .var for which per-cell percentage metrics are computed (e.g. "mito" to compute pct_counts_mito). |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output -o | file required output | Output h5mu file. |
--output_compression | string | Compression format to use for the output AnnData and/or Mudata objects. By default no compression is applied. |
Options
Name | Type & Properties | Description |
|---|---|---|
--expr_type | string | Name of the expression unit, used to build the metric keys. |
--var_type | string | Name of the variable type, used to build the metric keys. |
--log1p | boolean | Also compute log1p-transformed quality control metrics. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
modality: [ "rna" ]
output: "$id.$key.output"
expr_type: [ "counts" ]
var_type: [ "genes" ]
log1p: [ true ]
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline_rapids.git \
-revision v0.1.3 \
-main-script target/nextflow/preprocessing/calculate_qc_metrics/main.nf \
-params-file params.yaml Relationships
Used by
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No components use this component.
Current component
preprocessing/calculate_qc_metricsopenpipeline_rapids v0.1.3
Uses
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