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removed -f from cutadapt, not compatible with -j
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@fjames003
fjames003 committed Feb 27, 2019
1 parent 042e4cb commit 6eeb175
Showing 1 changed file with 10 additions and 10 deletions.
20 changes: 10 additions & 10 deletions trim_galore
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Original file line number Diff line number Diff line change
Expand Up @@ -612,7 +612,7 @@ sub trim{
warn " >>> Now performing adaptive quality trimming with a Phred-score cutoff of: $cutoff <<<\n\n";
# sleep (1);

open (QUAL,"$path_to_cutadapt -j $cores -f fastq -e $error_rate -q $cutoff -a X $filename |") or die "Can't open pipe to Cutadapt: $!";
open (QUAL,"$path_to_cutadapt -j $cores -e $error_rate -q $cutoff -a X $filename |") or die "Can't open pipe to Cutadapt: $!";

my $qual_count = 0;

Expand Down Expand Up @@ -691,19 +691,19 @@ sub trim{
if ( scalar(@filenames)%2 == 0){ # this is read 1 of a pair
warn "\n >>> Now performing adapter trimming for the adapter sequence: '$adapter' from file $temp <<< \n";
#sleep (1);
$pid = open3 (\*WRITER, \*TRIM, \*ERROR,"$path_to_cutadapt -j $cores -f fastq -e $error_rate -O $stringency -a $adapter $output_dir$temp") or die "Failed to launch Cutadapt: $!\n";
$pid = open3 (\*WRITER, \*TRIM, \*ERROR,"$path_to_cutadapt -j $cores -e $error_rate -O $stringency -a $adapter $output_dir$temp") or die "Failed to launch Cutadapt: $!\n";
}
else{ # this is read 2 of a pair
warn "\n >>> Now performing adapter trimming for the adapter sequence: '$a2' from file $temp <<< \n";
#sleep (1);
$pid = open3 (\*WRITER, \*TRIM, \*ERROR,"$path_to_cutadapt -j $cores -f fastq -e $error_rate -O $stringency -a $a2 $output_dir$temp") or die "Failed to launch Cutadapt: $!\n";
$pid = open3 (\*WRITER, \*TRIM, \*ERROR,"$path_to_cutadapt -j $cores -e $error_rate -O $stringency -a $a2 $output_dir$temp") or die "Failed to launch Cutadapt: $!\n";
}
}
### Using the same adapter for both read 1 and read 2
else{
warn "\n >>> Now performing adapter trimming for the adapter sequence: '$adapter' from file $temp <<< \n";
# sleep (3);
$pid = open3 (\*WRITER, \*TRIM, \*ERROR,"$path_to_cutadapt -j $cores -f fastq -e $error_rate -O $stringency -a $adapter $output_dir$temp") or die "Failed to launch Cutadapt: $!\n";
$pid = open3 (\*WRITER, \*TRIM, \*ERROR,"$path_to_cutadapt -j $cores -e $error_rate -O $stringency -a $adapter $output_dir$temp") or die "Failed to launch Cutadapt: $!\n";
}

close WRITER or die $!; # not needed
Expand Down Expand Up @@ -868,20 +868,20 @@ sub trim{
### Figure out whether current file counts as read 1 or read 2 of paired-end files
if ( scalar(@filenames)%2 == 0){ # this is read 1 of a pair
warn "\n >>> Now performing Poly-A trimming for the adapter sequence: '$adapter' from file $temp <<< \n";
$pid = open3 (\*WRITER, \*TRIM, \*ERROR,"$path_to_cutadapt -j $cores -f fastq -e $error_rate -O $stringency -a $adapter $output_dir$temp") or die "Failed to launch Cutadapt: $!\n";
$pid = open3 (\*WRITER, \*TRIM, \*ERROR,"$path_to_cutadapt -j $cores -e $error_rate -O $stringency -a $adapter $output_dir$temp") or die "Failed to launch Cutadapt: $!\n";
}
else{ # this is read 2 of a pair
$isR2 = 1;
warn "\n >>> Now performing Poly-A trimming for the adapter sequence: '$a2' from file $temp <<< \n";
# For Read 2 we need to trim the PolyT (or PolyA) from the 5' end instead! Hence -g $a2 and not -a!
$pid = open3 (\*WRITER, \*TRIM, \*ERROR,"$path_to_cutadapt -j $cores -f fastq -e $error_rate -O $stringency -g $a2 $output_dir$temp") or die "Failed to launch Cutadapt: $!\n";
$pid = open3 (\*WRITER, \*TRIM, \*ERROR,"$path_to_cutadapt -j $cores -e $error_rate -O $stringency -g $a2 $output_dir$temp") or die "Failed to launch Cutadapt: $!\n";
}
}
### Using the same adapter for both read 1 and read 2 - Single end will use the same adapters are Read 1s for paired-end files
else{
warn "\n >>> Now performing single-end Poly-A trimming for with the sequence: '$adapter' from file $temp <<< \n";
# sleep (3);
$pid = open3 (\*WRITER, \*TRIM, \*ERROR,"$path_to_cutadapt -j $cores -f fastq -e $error_rate -O $stringency -a $adapter $output_dir$temp") or die "Failed to launch Cutadapt: $!\n";
$pid = open3 (\*WRITER, \*TRIM, \*ERROR,"$path_to_cutadapt -j $cores -e $error_rate -O $stringency -a $adapter $output_dir$temp") or die "Failed to launch Cutadapt: $!\n";
}

close WRITER or die $!; # not needed
Expand Down Expand Up @@ -1023,19 +1023,19 @@ sub trim{
if ( scalar(@filenames)%2 == 0){ # this is read 1 of a pair
warn "\n >>> Now performing quality (cutoff '$quality_cutoff') and adapter trimming in a single pass for the adapter sequence: '$adapter' from file $filename <<< \n";
#sleep (1);
$pid = open3 (\*WRITER, \*TRIM, \*ERROR, "$path_to_cutadapt -j $cores -f fastq -e $error_rate $quality_cutoff -O $stringency $trim_n -a $adapter $filename") or die "Failed to launch Cutadapt: $!";
$pid = open3 (\*WRITER, \*TRIM, \*ERROR, "$path_to_cutadapt -j $cores -e $error_rate $quality_cutoff -O $stringency $trim_n -a $adapter $filename") or die "Failed to launch Cutadapt: $!";
}
else{ # this is read 2 of a pair
warn "\n >>> Now performing quality (cutoff '$quality_cutoff') and adapter trimming in a single pass for the adapter sequence: '$a2' from file $filename <<< \n";
#sleep (1);
$pid = open3 (\*WRITER, \*TRIM, \*ERROR, "$path_to_cutadapt -j $cores -f fastq -e $error_rate $quality_cutoff -O $stringency $trim_n -a $a2 $filename") or die "Failed to launch Cutadapt: $!";
$pid = open3 (\*WRITER, \*TRIM, \*ERROR, "$path_to_cutadapt -j $cores -e $error_rate $quality_cutoff -O $stringency $trim_n -a $a2 $filename") or die "Failed to launch Cutadapt: $!";
}
}
### Using the same adapter for both read 1 and read 2
else{
warn "\n >>> Now performing quality (cutoff '$quality_cutoff') and adapter trimming in a single pass for the adapter sequence: '$adapter' from file $filename <<< \n";
#sleep (1);
$pid = open3 (\*WRITER, \*TRIM, \*ERROR, "$path_to_cutadapt -j $cores -f fastq -e $error_rate $quality_cutoff -O $stringency $trim_n -a $adapter $filename") or die "Failed to launch Cutadapt: $!";
$pid = open3 (\*WRITER, \*TRIM, \*ERROR, "$path_to_cutadapt -j $cores -e $error_rate $quality_cutoff -O $stringency $trim_n -a $adapter $filename") or die "Failed to launch Cutadapt: $!";
}

close WRITER or die $!; # not needed
Expand Down

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