bin/seqtrimnext in seqtrimnext-2.0.59 vs bin/seqtrimnext in seqtrimnext-2.0.60

@@ -117,11 +117,11 @@
 #Checks install requeriments
 require 'install_requirements'
 
 ins = InstallRequirements.new
 if (!ins.check_install_requirements)
-  exit
+  exit(-1)
 end
 
 require "logger"
 require 'optparse'
 require "global_match"
@@ -376,11 +376,11 @@
   exit
 end
 
 if !File.exists?($FORMATTED_DB_PATH)
   STDERR.puts "Database path not found: #{$FORMATTED_DB_PATH}. \n\n\nInstall databases to this path or set your BLASTDB environment variable (eg.: export BLASTDB=new_path)"
-  exit
+  exit(-1)
 end
 
 
 if options[:check_db] then
   # check and format blast databases
@@ -393,21 +393,21 @@
 # if ((ARGV.count != 2) && (ARGV.count != 3)) # con esto vemos si hay argumentos,
 if (ARGV.count != 0) || (!required_options) # con esto vemos si hay argumentos,
   puts "You must provide all required options"
   puts ""
   puts optparse.help
-  exit
+  exit(-1)
 end
 
 # check for template
 if (!File.exists?(options[:template]))
   if File.exists?(File.join($SEQTRIM_PATH,'templates',options[:template]))
     options[:template] = File.join($SEQTRIM_PATH,'templates',options[:template])
   else
     $LOG.info "Params file: #{options[:template]} doesn't exists. \n\nYou can use your own template or specify one from this list:\n============================="
     puts Dir.glob(File.join($SEQTRIM_PATH,'templates','*.txt')).map{|t| File.basename(t)}
-    exit
+    exit(-1)
   end
 end
 $LOG.info "Using init file: #{$SEQTRIMNEXT_INIT}"
 $LOG.info "Using params file: #{options[:template]}"
 
@@ -416,24 +416,24 @@
 if options[:fastq]
   options[:fastq].each do |fastq_file|
     # fastq file
     if (!fastq_file.nil? && fastq_file!='-' && !File.exists?(File.expand_path(fastq_file)))
       $LOG.error "Input file: #{fastq_file} doesn't exists"
-      exit
+      exit(-1)
     end
   end
 end
 
 # fasta file
 if (!options[:fasta].nil? && !File.exists?(options[:fasta]))
   $LOG.error "Input file: #{options[:fasta]} doesn't exists"
-  exit
+  exit(-1)
 end
 
 # qual file
 if ((!options[:qual].nil?)&&(!File.exists?(options[:qual])))
   $LOG.error "Input file: #{options[:qual]} doesn't exists"
-  exit
+  exit(-1)
 end
 
 s = Seqtrim.new(options)
 
 #generate report