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. Most processed outputs are nested by sample and variant callers, i.e. ⁠*VariantCalling/<TUMOR_vs_NORMAL>/<CALLER>⁠. Other times the data is organized as ⁠*VariantCalling/<CALLER>/<TUMOR_vs_NORMAL>⁠. This walks through the output destination (URI of ⁠*VariantCalling⁠) with similar intention to map_sample_output_rnaseq, but for Sarek outputs.

Usage

map_sample_output_sarek(syn_out, sample_level = 2)

Arguments

syn_out	Syn id of syn output destination with files of interest.
sample_level	If caller is organized by sample, use 2 (default), if samples organized by caller, use 3. See details.

Details

Note: And additional step post-Sarek will create MAFs in the output subdirectory DeepVariant. If this is run after the MAF creation step, this will return file indexes with those .maf files.

Value

A data.table with cols caller caller_path caller_syn output_name output_id sample workflow

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