remanifest: Reconstitute a manifest
In nf-osi/nfportalutils: NF Portal Utilities

remanifest

R Documentation

Reconstitute a manifest

Description

Quickly "reconstitute" a manifest for files with existing annotations. This is a power-user alternative to schematic's manifest_generate with option useAnnotations = TRUE for certain scenarios:

Usage

remanifest(scope, file = "manifest.csv", recurse = TRUE, mf = data.table())

Arguments

`scope`	Synapse id of something representing one or more datasets. Can be a folder or Synapse dataset entity.
`file`	Name of file to be written. Use `NULL` to return the `data.table` instead of writing to file.
`recurse`	Include everything nested within folder scope, default `TRUE`, or only the immediate files. Not used if dataset is Synapse dataset entity.
`mf`	Intermediate manifest to build upon; used when recursive.

Details

Meant to be faster and more convenient for workflows focused on scalable/programmatic annotation/revalidation. Convenience and speed mainly comes from bypassing the schematic API layer and using the Synapse API directly, so manifest is reconstituted directly as R data.table instead of having to download a Googlesheets or Excel intermediate. The result .csv is still intended to be schematic-compatible for validation via manifest_validate.
Works with both a Synapse dataset entity as well as a folder; schematic currently only handles the latter (the folder concept predates Synapse datasets).
If folder-scoped, can choose between generating manifest with just immediate files or, like schematic, nested files. This is useful, for example, if the main scope folder is "RNA-seq" and the main files are fastqs, but there is a child folder called "md5" with md5 files, and the manifest is really meant for the fastqs.
Does not try to download synapse_manifest.csv, which can be useful to regenerate a manifest when ARs have been set.
Does not require an asset view.

Other developer notes: See also gather_annotations for the under-the-hood workhorse. Intended for further development to be used as part of advanced annotation utils.

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