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