metadata/join_csv

Description

Join a csv containing metadata to the .obs or .var field of a mudata file.

Type

python_script

Contributors

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "rna" ]  
output: "$id.$key.output.h5mu"  
csv_key: [ "id" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.4 \  
  -main-script target/nextflow/metadata/join_csv/main.nf \  
  -params-file params.yaml

MuData Input

Name	Type & Properties	Description
--input -i	file required	Input h5mu file
--modality	string
--obs_key	string	Obs column name where the sample id can be found for each observation to join on. Useful when adding metadata to concatenated samples. Mutually exclusive with `--var_key`."
--var_key	string	Var column name where the sample id can be found for each variable to join on. Mutually exclusive with `--obs_key`."

Name

Type & Properties

--input

-i

file

required

--modality

string

--obs_key

string

--var_key

string

MuData Output

Name	Type & Properties	Description
--output -o	file required output	Output h5mu file.
--output_compression	string	The compression format to be used on the output h5mu object.

Name

Type & Properties

--output

-o

file

required

output

--output_compression

string

Metadata Input

Name	Type & Properties	Description
--input_csv	file required	.csv file containing metadata
--csv_key	string	column of the the csv that corresponds to the sample id.

Name

Type & Properties

--input_csv

file

required

--csv_key

string