filter/filter_with_counts

Description

Filter scRNA-seq data based on the primary QC metrics.
This is based on both the UMI counts, the gene counts
and the mitochondrial genes (genes starting with mt/MT).

Type

python_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "rna" ]  
output: "$id.$key.output.h5mu"  
obs_name_filter: [ "filter_with_counts" ]  
var_name_filter: [ "filter_with_counts" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.2.0 \  
  -main-script target/nextflow/filter/filter_with_counts/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required	Input h5mu file
--modality	string	Which modality from the input MuData file to process.
--layer	string	Location of the count matrix. If specified, will be used to select a key from .layers, otherwise .X is used.

Name

Type & Properties

--input

file

required

--modality

string

--layer

string

Outputs

Name	Type & Properties	Description
--output	file output	Output h5mu file.
--do_subset	boolean_true	Whether to subset before storing the output.
--obs_name_filter	string	In which .obs slot to store a boolean array corresponding to which observations should be removed.
--var_name_filter	string	In which .var slot to store a boolean array corresponding to which variables should be removed.
--output_compression	string	Compression format to use for the output AnnData and/or Mudata H5 files. By default no compression is applied.

Name

Type & Properties

--output

file

output

--do_subset

boolean_true

--obs_name_filter

string

--var_name_filter

string

--output_compression

string

Arguments

Name	Type & Properties	Description
--min_counts	integer	Minimum number of counts captured per cell.
--max_counts	integer	Maximum number of counts captured per cell.
--min_genes_per_cell	integer	Minimum of non-zero values per cell.
--max_genes_per_cell	integer	Maximum of non-zero values per cell.
--min_cells_per_gene	integer	Minimum of non-zero values per gene.

Name

Type & Properties

--min_counts

integer

--max_counts

integer

--min_genes_per_cell

integer

--max_genes_per_cell

integer

--min_cells_per_gene

integer