derive_annotations: Derive annotations for processed output data

In nf-osi/nfportalutils: NF Portal Utilities

Derive annotations for processed output data

Description

A processed or derived file can inherit annotations from the input file(s). Currently, this generously facilitates inheritance of many properties except ones that "obviously" shouldn't be inherited, such as "fileFormat" or "comments". These rules are hard-coded and might need to be expanded as the data model changes, and the manifest generated should still be reviewed.

Usage

derive_annotations(sample_io, template, schema, format, verbose = TRUE)

Arguments

format

File format of the processed data, e.g. "vcf".

Details

If multiple inputs given, this will inherit annotations from the FIRST input. Files that pass through this naturally have dataSubtype automatically set to "processed" and fileFormat set to the actual new file format. In the future, template itself may define default format so we don't need to specify explicitly.

nf-osi/nfportalutils documentation built on Feb. 26, 2024, 1:05 p.m.