Join csv

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

Info

ID: join_csv
Namespace: metadata

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/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 1.0.1 -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)