Skip to contents

Check fastq read pair matches samplesheet read pair assignment.

Source: R/nextflow_testing_utils.R
check_readpair_validity.Rd

Read pairs are often encoded in the name of the file. Here, we check that if encoded in the name of the file, that the samplesheet read pair (e.g. _1 or _2) matches

Usage

check_readpair_validity(
  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.

Examples

if (FALSE) {
 check_readpair_validity('syn39542932')
 check_readpair_validity('syn29530880')
}