Assemble File Details. — assemble_file

Update the database by appending to the gambl_files table.

assemble_file_details(
  file_details_df,
  file_paths,
  tool_name,
  unix_group,
  these_sample_ids,
  output_type = "ploidy",
  is_production = "yes"
)

Arguments

file_details_df: Optionally supply the data frame directly instead (e.g. from find_files_extract_wildcards).
file_paths: A vector of full file paths, e.g. the output of dir.
tool_name: The tool or pipeline that generated the files (should be the same for all).
unix_group: The unix group (should be the same for all).
these_sample_ids: A vector of sample_id the same length and in the same order as the file paths.
output_type: The file type to distinguish different output file types from the same pipeline (e.g. seg, maf, ploidy).
is_production: Boolean parameter. Default is yes.

Value

Updates the database by appending to the gambl_files table. Use with caution!

Details

Specify the file paths with file_paths followed by the name of the tool (tool_name). Next, set the output type (e.g seq, maf, etc.) and unix group (should be the same for all). Lastly, specify the sample IDs with these_sample_ids. For more information on how to use the optional parameters, refer to the parameter descriptions.

Examples

if (FALSE) {
assemble_file_details(file_paths = c(one.maf, another.maf), 
                      tool_name = "manta",
                      unix_group = "genome",
                      output_type = "maf",
                      these_sample_ids = c(one_sample, another_sample))
}