Binning

Conversion of (pre-processed) expression count data into relative values (bins) to address scale differences across sequencing batches

Info

ID: binning
Namespace: scgpt

Links

Source

Example commands

You can run the pipeline using nextflow run.

View help

You can use --help as a parameter to get an overview of the possible parameters.

nextflow run openpipelines-bio/openpipeline \
  -r 2.1.1 -latest \
  -main-script target/nextflow/scgpt/binning/main.nf \
  --help

Run command

Example of params.yaml

# Inputs
input: # please fill in - example: "input.h5mu"
modality: "rna"
# input_layer: "foo"
var_input: "id_in_vocab"
n_input_bins: 51

# Outputs
# output: "$id.$key.output.h5mu"
# output_compression: "gzip"
output_obsm_binned_counts: "binned_counts"
# seed: 123

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"

# Arguments

nextflow run openpipelines-bio/openpipeline \
  -r 2.1.1 -latest \
  -profile docker \
  -main-script target/nextflow/scgpt/binning/main.nf \
  -params-file params.yaml

Note

Replace -profile docker with -profile podman or -profile singularity depending on the desired backend.

Argument groups

Inputs

Name	Description	Attributes
--input	Input h5mu file.	file, required, example: "input.h5mu"
--modality		string, default: "rna"
--input_layer	Mudata layer (key from .layers) to use as input data for binning. If not specified, .X is used.	string
--var_input	The name of the adata.var column containing boolean mask for vocabulary-cross checked and/or highly variable genes.	string, default: "id_in_vocab"
--n_input_bins	The number of bins to discretize the data into. When no value is provided, data won’t be binned.	integer, default: 51

Outputs

Name	Description	Attributes
--output	The output h5mu file containing the binned data.	file, required, example: "output.h5mu"
--output_compression	The compression algorithm to use for the output h5mu file.	string, example: "gzip"
--output_obsm_binned_counts	The name of the adata layer to write the binned data to.	string, default: "binned_counts"
--seed	Seed for random number generation.	integer

Authors

• Dorien Roosen (maintainer, author)

• Elizabeth Mlynarski (author)

• Weiwei Schultz (contributor)