query/cellxgene_census

Description

Query cells from a CellxGene Census or custom TileDBSoma object.
Aside from fetching the cells' RNA counts (.X), cell metadata
(.obs) and gene metadata (.var), this component also fetches
the dataset metadata and joins it into the cell metadata.

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'  
cell_filter_min_genes: [ 50 ]  
cell_filter_min_counts: [ 0 ]  
gene_filter_min_cells: [ 5 ]  
gene_filter_min_counts: [ 0 ]  
output: "$id.$key.output.h5mu"  
output_modality: [ "rna" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v3.0.2 \  
  -main-script target/nextflow/query/cellxgene_census/main.nf \  
  -params-file params.yaml

Input database

Name	Type & Properties	Description
--input_uri	string	If specified, a URI containing the Census SOMA objects. If specified, will take precedence over the `--census_version` argument.
--census_version	string	Which release of CellxGene census to use. Possible values are "latest", "stable", or the date of one of the releases (e.g. "2023-07-25"). For more information, check the documentation on [Census data releases](https://chanzuckerberg.github.io/cellxgene-census/cellxgene_census_docsite_data_release_info.html).
--add_dataset_metadata	boolean_true	If true, the experiment metadata will be added to the cell metadata. More specifically: `collection_id`, `collection_name`, `collection_doi`, `dataset_title`.

Name

Type & Properties

--input_uri

string

--census_version

string

--add_dataset_metadata

boolean_true

Cell query

Name	Type & Properties	Description
--species	string required	The organism to query, usually one of `Homo sapiens` or `Mus musculus`.
--obs_value_filter	string required	Filter for selecting the `obs` metadata (i.e. cells). Value is a filter query written in the SOMA `value_filter` syntax.

Name

Type & Properties

--species

string

required

--obs_value_filter

string

required

Filter cells by grouping

Name	Type & Properties	Description
--cell_filter_grouping	string multiple	A subset of 'obs' columns by which to group the cells for filtering. Only groups surpassing or equal to the `--cell_filter_minimum_count` threshold will be retained. Take care not to introduce a selection bias against cells with more fine-grained ontology annotations.
--cell_filter_minimum_count	integer	A minimum number of cells per group to retain. If `--cell_filter_grouping` is defined, this parameter should also be provided and vice versa.

Name

Type & Properties

--cell_filter_grouping

string

multiple

--cell_filter_minimum_count

integer

Count filtering

Name	Type & Properties	Description
--cell_filter_min_genes	integer	Remove cells with less than this number of genes.
--cell_filter_min_counts	integer	Remove cells with less than this number of counts.
--gene_filter_min_cells	integer	Remove genes expressed in less than this number of cells.
--gene_filter_min_counts	integer	Remove genes with less than this number of counts.

Name

Type & Properties

--cell_filter_min_genes

integer

--cell_filter_min_counts

integer

--gene_filter_min_cells

integer

--gene_filter_min_counts

integer

Outputs

Name	Type & Properties	Description
--output	file required output	Output h5mu file.
--output_modality	string	Which modality to store the output in.
--output_layer_counts	string	Which layer to store the raw counts in. If not provided, the .X layer will be used.
--output_compression	string	Compression format to use for the output AnnData and/or Mudata objects. By default no compression is applied.

Name

Type & Properties

--output

file

required

output

--output_modality

string

--output_layer_counts

string

--output_compression

string