Move obsm to obs

Move a matrix from .obsm to .obs.


ID: move_obsm_to_obs
Namespace: metadata

Newly created columns in .obs will be created from the .obsm key suffixed with an underscore and the name of the columns of the specified .obsm matrix

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 1.0.1 -latest \
  -main-script target/nextflow/metadata/move_obsm_to_obs/ \

Run command

Example of params.yaml
# MuData Input
input: # please fill in - example: "input.h5mu"
modality: "rna"
obsm_key: # please fill in - example: "foo"

# MuData Output
# output: "$id.$key.output.h5mu"
# output_compression: "gzip"

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"
nextflow run openpipelines-bio/openpipeline \
  -r 1.0.1 -latest \
  -profile docker \
  -main-script target/nextflow/metadata/move_obsm_to_obs/ \
  -params-file params.yaml

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

Argument groups

MuData Input

Name Description Attributes
--input Input h5mu file file, required, example: "input.h5mu"
--modality string, default: "rna"
--obsm_key Key of a data structure to move from .obsm to .obs. string, required

MuData Output

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


  • Dries Schaumont (author)