map_sample_output_sarek: Map sample to output from nf-sarek

In nf-osi/nfportalutils: NF Portal Utilities

Map sample to output from nf-sarek

Description

See https://nf-co.re/sarek. Similar to map_sample_output_rnaseq but for Sarek outputs. Processed outputs have been seen to have variable organization, nested first by sample or by caller as ⁠VariantCalling/<SAMPLE>/<CALLER>⁠ or as ⁠VariantCalling/<CALLER>/<SAMPLE>⁠. The hierarchy/context needed for annotation can be obtained with a fileview and given the necessary starting point syn_out, which is the id of the relevant output folder (called VariantCalling or variant_calling usually).

Usage

map_sample_output_sarek(
  syn_out,
  fileview,
  output = c("CNVkit", "DeepVariant", "Strelka2", "Mutect2", "FreeBayes")
)

Arguments

syn_out	Syn id of variant calling output folder.
fileview	An existing fileview to use (usually the project's local fileview) that scopes outputs and has "default" columns (id, name, type, parentId, path, ...). See details.
output	Which output to select and annotate. Defaults to checking the presence of possible prioritized outputs ("CNVkit", "DeepVariant", "Strelka2", "Mutect2", and "FreeBayes"), though typically only a subset makes sense and can be explicitly specified, which also speeds up results.

Details

Note: Depending on when map_sample_output_sarek is run on the output directory, there may be just vcf or both vcf and maf present. maf are ignored since technically it is not an output of sarek but from further processing with nf-vcf2maf.

Value

A data.table with cols caller path output_name output_id sample workflow. An attribute workflow=nf-sarek will be set on the returned list, and elements will have attribute outputFrom set, e.g. outputFrom=CNVkit.

nf-osi/nfportalutils documentation built on June 10, 2025, 5:08 a.m.