nf_sarek_datasets: Create datasets for Sarek-called somatic or germline variants...

In nf-osi/nfportalutils: NF Portal Utilities

Create datasets for Sarek-called somatic or germline variants results

Description

Organize variant call files from Nextflow Sarek into 3-4 datasets, grouping files by variant type and workflow with titles having the format: "type Genomic Variants - workflow Pipeline", e.g. "Somatic Genomic Variants - Strelka Pipeline". As you can see, this assumes that you want to create datasets that segregate Somatic and Germline calls. This makes sense for NF because Germline calls can be treated differently. This uses latest version of all files and creates a Draft version of the dataset.

Usage

nf_sarek_datasets(
  output_map,
  parent,
  workflow = c("FreeBayes", "Mutect2", "Strelka", "DeepVariant"),
  verbose = TRUE,
  dry_run = TRUE
)

Arguments

output_map	The data.table returned from map_sample_output_sarek. See details for alternatives.
parent	Synapse id of parent project where the dataset will live.
workflow	One of workflows used.
verbose	Optional, whether to be verbose – defaults to TRUE.
dry_run	If TRUE, don't actually store dataset, just return the data object for inspection or further modification.

Details

Since we basically just need the syn entity id, variant type, and workflow to group the files. Instead of getting this info through running ⁠map_*⁠ as in the example, you may prefer using a fileview, in which case you just need to download a table from a fileview that has id => output_id + the dataType and workflow annotations. The fileview can be used after the files are annotated. If you want to create datasets before files are annotated, then you have to use ⁠map_*⁠.

Finally, datasets cannot use the same name if stored in the same project, so if there are multiple batches, the names will have to be made unique by adding the batch number, source data id, processing date, or whatever makes sense.

Value

A list of dataset objects.

Examples

## Not run: 
syn_out <- "syn26648589"
m <- map_sample_output_sarek(syn_out)
datasets <- nf_sarek_datasets(m, parent = "syn26462036", dry_run = F) # use a test project

## End(Not run)

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