#!/usr/bin/perl -w
use strict;

# this script was made with consideration for UMI-deduplicating.
# this is because there are three .fastq files for each sample. 
# the provider states the info about which file contains which info,
# but in our case, from GenomeScan in Leiden, R2 contains the UMI read.
# R1 and R3 contain sequencing information from paired-end sequencing

foreach my $file1 ( <*_R1.fastq.gz> ) {
    my $file2 = $file1;
    $file2 =~ s/\_R1\./_R2./;
    my $file3 =~ s/\_R3\./_R2./;
    die "file1==file2" if $file1 eq $file2;
    my $sample = $file1;
    $sample =~ s/\_R1\.fastq\.gz$//;
    mkdir $sample.'_R1', 0700;
    system join(' ', 'fastqc', '-o', $sample.'_R1', $file1);
    mkdir $sample.'_R2', 0700;
    system join(' ', 'fastqc', '-o', $sample.'_R2', $file2);
    mkdir $sample.'_R3', 0700;
    system join(' ', 'fastqc', '-o', $sample.'_R3', $file3)
}