This should be run in an existing dataset package root.
Arguments
- clinical_data
Clinical table query.
- ref_map
YAML file specifying the mapping of (NF) clinical metadata to cBioPortal model. See details.
- verbose
Whether to provide informative messages throughout.
Details
Clinical data are mapped and exported according to a reference mapping.
Also reformatting of PATIENT_ID
, SAMPLE_ID
to contain only letters, numbers, points, underscores, hyphens;
in Nextflow processing any spaces gets replaced with underscores so that's the default here.
Does not check for missing samples, as final validation via cBioPortal tool is still expected for that.