dataflow/concatenate_h5mu

Description

Concatenate observations from samples in several (uni- and/or multi-modal) MuData files into a single file.

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'  
output: "$id.$key.output.h5mu"  
obs_sample_name: [ "sample_id" ]  
other_axis_mode: [ "move" ]  
uns_merge_mode: [ "make_unique" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.3 \  
  -main-script target/nextflow/dataflow/concatenate_h5mu/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input -i	file required multiple	Paths to the different samples to be concatenated.
--modality	string multiple	Only output concatenated objects for the provided modalities. Outputs all modalities by default.
--input_id	string multiple	Names of the different samples that have to be concatenated. Must be specified when using '--mode move'. In this case, the ids will be used for the columns names of the dataframes registring the conflicts. If specified, must be of same length as `--input`.
--output -o	file output	Output location for the concatenated MuData object file.
--obs_sample_name	string	Name of the .obs key under which to add the sample names.
--other_axis_mode	string	How to handle the merging of other axis (var, obs, ...). - None: keep no data - same: only keep elements of the matrices which are the same in each of the samples - unique: only keep elements for which there is only 1 possible value (1 value that can occur in multiple samples) - first: keep the annotation from the first sample - only: keep elements that show up in only one of the objects (1 unique element in only 1 sample) - move: identical to 'same', but moving the conflicting values to .varm or .obsm
--uns_merge_mode	string	How to handle the merging of .uns across modalities - None: keep no data - same: only keep elements of the matrices which are the same in each of the samples - unique: only keep elements for which there is only 1 possible value (1 value that can occur in multiple samples) - first: keep the annotation from the first sample - only: keep elements that show up in only one of the objects (1 unique element in only 1 sample) - make_unique: identical to 'unique', but keys which are not unique are made unique by prefixing them with the sample id.
--obsp_keys	string multiple	List of `.obsp` keys for which block-diagonal concatenation should be performed. If not provided, no `.obsp` keys will be concatenated. Provided keys must be present in all samples for block concatenation to be performed.
--output_compression	string	Compression format to use for the output AnnData and/or Mudata objects. By default no compression is applied.

Name

Type & Properties

--input

-i

file

required

multiple

--modality

string

multiple

--input_id

string

multiple

--output

-o

file

output

--obs_sample_name

string

--other_axis_mode

string

--uns_merge_mode

string

--obsp_keys

string

multiple

--output_compression

string