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Samplesheets are used in rnaseq pipelines, defined here: https://nf-co.re/rnaseq/usage#full-samplesheet. After the pipeline is run, it should be found in an output folder called pipeline_info. This is a simple helper to get a mapping of sample ids to input files (either one-to-many or one-to-one) as a table.

Usage

map_sample_input_ss(
  samplesheet,
  parse_fun = function(x) gsub("_T[0-9]$", "", x)
)

Arguments

samplesheet

A local file or syn id of samplesheet.

parse_fun

Function implementing how to parse samples in samplesheet.