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.