map_sample_input_ss: Parse nextflow samplesheet for sample inputs

In nf-osi/nfportalutils: NF Portal Utilities

Parse nextflow samplesheet for sample inputs

Description

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.

nf-osi/nfportalutils documentation built on Feb. 26, 2024, 1:05 p.m.