Make annotations from workflow tool stats — annotate_with_tool

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)