write default values to drake_params.tsv for phipmake pipeline

write_drake_params(dir, screen_name, counts_filename = "counts.csv",
  counts_type = "Counts", enrichment_filename = "enrichment.csv",
  enrichment_type = "Enrichment", enrichment_threshold = 5,
  metadata_path = "/data/hlarman1/PhIPdb/Metadata/PeptideLibraries",
  output_extension = ".tsv")

Arguments

dir

PhIP-seq project directory.

screen_name

Identifier for multiplexed screen, e.g. phipseq_0001.

counts_filename

Name of demultiplexed, merged reads file in screen directory.

counts_type

Identifier for type of counts data to append in output file names.

enrichment_filename

Name of demultiplexed, merged enrichment file in screen directory.

enrichment_type

Identifier for type of enrichment data to append in output file names.

enrichment_threshold

Threshold enrichment value for determining hits.

metadata_path

Directory path string to metadata folder containing peptide files and intrapeptide blast alignment files.

output_extension

Extension for tab-separated output files.