dataflow/concat

Description

Concatenates several uni-modal samples in .h5mu files into a single file.

Type

python_script

Contributors

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" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.0 \  
  -main-script target/nextflow/dataflow/concat/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input -i	file required multiple	Paths to the different samples to be concatenated.
--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_compression	string	The compression format to be used on the output h5mu object.
--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

Name

Type & Properties

--input

-i

file

required

multiple

--input_id

string

multiple

--output

-o

file

output

--output_compression

string

--obs_sample_name

string

--other_axis_mode

string