annotate_with_tool_stats: Make annotations from workflow tool stats
In nf-osi/nfportalutils: NF Portal Utilities

annotate_with_tool_stats

R Documentation

Make annotations from workflow tool stats

Description

Extracts a subset of samtools stats and picard stats from workflow metafiles to surface as annotations. Note: picard stats only for WGS/WES/targeted sequencing. Regarding the selection of stats, see the Genomic Data Commons (GDC) model for Aligned Reads

Usage

annotate_with_tool_stats(
  samtools_stats_file = NULL,
  picard_stats_file = NULL,
  sample_io = NULL
)

Arguments

`samtools_stats_file`	Path to file/syn id of file with samtools stats produced by the workflow.
`picard_stats_file`	Path to file/syn id of file with picard stats produced by the workflow.
`sample_io`	Sample input and output mapping, used to assign stats to appropriate outputs (bam)