Add id

Add id of .obs.

Info

ID: add_id
Namespace: metadata

Links

Source

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 2.1.1 -latest \
  -main-script target/nextflow/metadata/add_id/main.nf \
  --help

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 2.1.1 -latest \
  -profile docker \
  -main-script target/nextflow/metadata/add_id/main.nf \
  -params-file params.yaml

Note

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

Argument group

Arguments

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

Authors

• Dries Schaumont (maintainer)