Fetch Output Files. — fetch_output

Get output files from a set of conditions.

fetch_output_files(
  tool,
  unix_group,
  base_path,
  results_dir = "99-outputs",
  seq_type = "genome",
  build = "hg38",
  search_pattern = "cellularity_ploidy.txt"
)

Arguments

tool: Name of tool.
unix_group: The unix group of the sample set.
base_path: Either the full or relative path to where all the results directories are for the tool e.g. "gambl/sequenza_current".
results_dir: Directory with results.
seq_type: Either genome or capture.
build: Default is hg38.
search_pattern: File-extensions search pattern.

Value

A data frame with one row per file and sample IDs parsed from the file name along with other GAMBL wildcards.

Details

This function lets the user specify multiple conditions for returning result subsets. First, specify the name of the tool with tool, then set the seq type (seq_type) to either genome or capture, together with the genome build (genome_build). A data frame will be returned with one row per file and sample IDs together with GAMBL wildcards.

Examples


ex_outs = fetch_output_files(tool = "manta",
                             base_path = "gambl/sequenza_current",
                             seq_type = "capture",
                             build = "hg38")