Subset obsp

Create a subset of an .obsp field in a mudata file, by filtering the columns based on the values of an .obs column.

Info

ID: subset_obsp
Namespace: filter

The resulting subset is moved to an .obsm slot

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/filter/subset_obsp/main.nf \
  --help

Run command

Example of params.yaml 
# Input
input: # please fill in - example: "input.h5mu"
modality: "rna"
input_obsp_key: # please fill in - example: "foo"
input_obs_key: # please fill in - example: "foo"
input_obs_value: # please fill in - example: "foo"

# Output
# output: "$id.$key.output.h5mu"
output_obsm_key: # please fill in - example: "foo"
# output_compression: "gzip"

# 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/filter/subset_obsp/main.nf \
  -params-file params.yaml
Note

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

Argument groups

Input

Name Description Attributes
--input Input h5mu file file, required, example: "input.h5mu"
--modality string, default: "rna"
--input_obsp_key The .obsp field to be filtered. string, required
--input_obs_key The .obs column to filter on. string, required
--input_obs_value The value to filter on in the .obs column. string, required

Output

Name Description Attributes
--output Output h5mu file. file, example: "output.h5mu"
--output_obsm_key The .obsm key to store the subset in. string, required
--output_compression The compression format to be used on the output h5mu object. string, example: "gzip"

Authors

  • Dorien Roosen (author, maintainer)