removed trimming option that was under construciton

#!/usr/bin/perl

#########################################

#                                       #

#     Written by Kai Battenberg         #

#     Plant Symbiosis Research Team     #

#                                       #

#########################################

use strict;

use warnings;

#####Options#####

my $barcodefile = $ARGV[0];

my $adjust_length = $ARGV[1];

my $cellranger_dir = $ARGV[2];

##########

#####Main#####

#make a hash of original and adjusted barcodes

my %barcodes;

open (ORIGINAL, "<$barcodefile") or die "cannot open $barcodefile.\n";

while (my $line = <ORIGINAL>) {

    my $original = $line;

    $original =~ s/\r//sig;

    $original =~ s/\n//sig;

    my $adjusted = $original;

    if ($adjust_length >= 0) {

        my $length = $adjust_length;

        $adjusted = substr ($length, 0, $adjusted);

    }

    else {

        my $length = abs ($adjust_length);

        my $As = "A" x $length;

        $adjusted = $As.$adjusted;

    }

    $barcodes{$adjusted} = $original;

}

close (ORIGINAL);

#get modified barcode list (raw)

my $raw_file = $cellranger_dir."/outs/raw_feature_bc_matrix/barcodes.tsv.gz";

my $modified_barcodes_raw = `zcat $raw_file | cut -f1 -d'-'`;

$modified_barcodes_raw =~ s/\n$//;

my @modified_barcodes_raw = split (/\n/, $modified_barcodes_raw);

#get modified barcode list (filtered)

my $filtered_file = $cellranger_dir."/outs/filtered_feature_bc_matrix/barcodes.tsv.gz";

my $modified_barcodes_filtered = `zcat $filtered_file | cut -f1 -d'-'`;

$modified_barcodes_filtered =~ s/\n$//;

my @modified_barcodes_filtered = split (/\n/, $modified_barcodes_filtered);

#replace barcodes

my $temp = "barcodes.txt";

open (TEMP, ">$temp") or die "cannot open $temp.\n";

foreach my $barcode (@modified_barcodes_raw) {

    print TEMP "$barcodes{$barcode}-1\n";

}

close (TEMP);

system "gzip -c $temp > $raw_file";

open (TEMP, ">$temp") or die "cannot open $temp.\n";

foreach my $barcode (@modified_barcodes_filtered) {

    print TEMP "$barcodes{$barcode}-1\n";

}

close (TEMP);

system "gzip -c $temp > $filtered_file";

unlink ($temp);

##########

install=false

######convert version#####

convertversion="0.3.0.90007"

convertversion="0.3.0.90008"

##########

fi

echo "Running launch_universc.sh in '$SDIR'"

BARCODERECOVER=${SDIR}/BarcodeRecovery.pl

BARCODERECOVER=${SDIR}/RecoverBarcodes.pl

PERCELLSTATS=${SDIR}/ExtractBasicStats.pl

##########

  -R2, --read2 FILE             Read 2 FASTQ file to pass to cellranger

  -f,  --file NAME              Path and the name of FASTQ files to pass to cellranger (prefix before R1 or R2)

                                e.g. /path/to/files/Example_S1_L001

  --trim                        run adapter and quality trimming on R2 files prior to running cellranger (underconstruction)

  -i,  --id ID                  A unique run id, used to name output folder

  -d,  --description TEXT       Sample description to embed in output files.

                exit 1

            fi

            ;;

        --trim)

            trim=true

            next=false

            shift

            ;;

       -i|--id)

            shift

            if [[ "$1" != "" ]]; then