Cross check genes

Cross-check genes with pre-trained scGPT model

Info

ID: cross_check_genes
Namespace: scgpt

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 2.1.0 -latest \
  -main-script target/nextflow/scgpt/cross_check_genes/main.nf \
  --help

Run command

Example of params.yaml 
# Inputs
input: # please fill in - example: "input.h5mu"
modality: "rna"
vocab_file: # please fill in - example: "resources_test/scgpt/vocab.json"
# input_var_gene_names: "gene_name"
# var_input: "foo"

# Outputs
# output: "$id.$key.output.h5mu"
# output_compression: "gzip"
output_var_filter: "id_in_vocab"

# Arguments
pad_token: "<pad>"

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"
nextflow run openpipelines-bio/openpipeline \
  -r 2.1.0 -latest \
  -profile docker \
  -main-script target/nextflow/scgpt/cross_check_genes/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 The input h5mu file containing of pre-processed data. file, required, example: "input.h5mu"
--modality The modality key of the MuData object containing the RNA AnnData object. string, default: "rna"
--vocab_file Model vocabulary file path. file, required, example: "resources_test/scgpt/vocab.json"
--input_var_gene_names The name of the adata.var column containing gene names. By default the .var index will be used. string, example: "gene_name"
--var_input .var column containing highly variable genes. If provided, will only cross-check HVG filtered genes with model vocabulary. string

Outputs

Name Description Attributes
--output The output cross-checked anndata file. file, required, example: "output.h5mu"
--output_compression string, example: "gzip"
--output_var_filter In which .var slot to store a boolean array corresponding to which observations should be filtered out based on HVG and model vocabulary. string, default: "id_in_vocab"

Arguments

Name Description Attributes
--pad_token The padding token used in the model. string, default: "<pad>"

Authors

  • Jakub Majercik (author)

  • Dorien Roosen (maintainer, author)

  • Elizabeth Mlynarski (author)

  • Weiwei Schultz (contributor)