Add id

Add id of .obs.


ID: add_id
Namespace: metadata

Also allows to make .obs_names (the .obs index) unique by prefixing the values with an unique id per .h5mu file

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 0.12.6 -latest \
  -main-script target/nextflow/metadata/add_id/ \

Run command

Example of params.yaml
# Arguments
input: # please fill in - example: "sample_path"
input_id: # please fill in - example: "foo"
obs_output: "sample_id"
# output: "$id.$key.output.h5mu"
# output_compression: "gzip"
make_observation_keys_unique: false

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"
nextflow run openpipelines-bio/openpipeline \
  -r 0.12.6 -latest \
  -profile docker \
  -main-script target/nextflow/metadata/add_id/ \
  -params-file params.yaml

Replace -profile docker with -profile podman or -profile singularity depending on the desired backend.

Argument group


Name Description Attributes
--input Path to the input .h5mu. file, required, example: "sample_path"
--input_id The input id. string, required
--obs_output Name of the .obs column where to store the id. string, default: "sample_id"
--output file, example: "output.h5mu"
--output_compression The compression format to be used on the output h5mu object. string, example: "gzip"
--make_observation_keys_unique Join the id to the .obs index (.obs_names). boolean_true


  • Dries Schaumont (maintainer)