check_readpair_validity: Check fastq read pair matches samplesheet read pair...

In nf-osi/nfportalutils: NF Portal Utilities

Check fastq read pair matches samplesheet read pair assignment.

Description

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

## Not run: 
 check_readpair_validity('syn39542932')
 check_readpair_validity('syn29530880')

## End(Not run)

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