<commit_before>#!/usr/bin/perl -w
##################################################################################################################################################
###This script is designed to run the various parts of the illumina 'pipeline' using a single .conf configuration file.
###
###
###Author: S.W.Boymans
###Latest change: ini parsing
###
###TODO:
##################################################################################################################################################

use strict;
use POSIX qw(tmpnam);
use Getopt::Long;

use illumina_prestats;
use illumina_mapping;
use illumina_poststats;
use illumina_realign;
use illumina_baseRecal;
use illumina_calling;
use illumina_filterVariants;
use illumina_annotateVariants;
use illumina_check;

### Check correct usage
die usage() if @ARGV == 0;

### initiate opt hash with settings
my %opt;
my $configurationFile;

%opt = (
    'RUNNING_JOBS'		=> {}, #do not use in .conf or .ini<commit_msg>Fix for loading perl modules<commit_after>#!/usr/bin/perl -w
##################################################################################################################################################
###This script is designed to run the various parts of the illumina 'pipeline' using a single .conf configuration file.
###
###
###Author: S.W.Boymans
###Latest change: ini parsing
###
###TODO:
##################################################################################################################################################

#### Load common perl modules ####
use strict;
use POSIX qw(tmpnam);
use Getopt::Long;
use FindBin;

#### Load pipeline modules ####
use lib "$FindBin::Bin"; #locates pipeline directory
use illumina_prestats;
use illumina_mapping;
use illumina_poststats;
use illumina_realign;
use illumina_baseRecal;
use illumina_calling;
use illumina_filterVariants;
use illumina_annotateVariants;
use illumina_check;

### Check correct usage
die usage() if @ARGV == 0;

### initiate opt hash with settings
my %opt;
my $configurationFile;

%opt = (
    'RUNNING_JOBS'		=> {}, #do not use in .conf or .ini
{'fraction_non_alphanumeric': 0.3643192488262911, 'fraction_numerical': 0.0009389671361502347, 'mean_word_length': 7.733606557377049, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3057961', 'n_tokens_mistral': 589, 'n_tokens_neox': 546, 'n_words': 176}