Join csv

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

Info

ID: join_csv
Namespace: metadata

Links

Source

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 1.0.2 -latest \
  -main-script target/nextflow/metadata/join_csv/main.nf \
  --help

Run command

Example of params.yaml

# MuData Input
input: # please fill in - example: "input.h5mu"
modality: "rna"
# obs_key: "foo"
# var_key: "foo"

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

# Metadata Input
input_csv: # please fill in - example: "metadata.csv"
csv_key: "id"

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"

nextflow run openpipelines-bio/openpipeline \
  -r 1.0.2 -latest \
  -profile docker \
  -main-script target/nextflow/metadata/join_csv/main.nf \
  -params-file params.yaml

Note

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"
--obs_key	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.”	string
--var_key	Var column name where the sample id can be found for each variable to join on. Mutually exclusive with --obs_key.”	string

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"

Metadata Input

Name	Description	Attributes
--input_csv	.csv file containing metadata	file, required, example: "metadata.csv"
--csv_key	column of the the csv that corresponds to the sample id.	string, default: "id"

Authors

• Dries Schaumont (author)