1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
|
Description: Change trimmomatic calls to TrimmomaticPE
Author: Nilesh Patra <nilesh@debian.org>
Forwarded: not-needed
Last-Update: 2022-03-11
--- a/bin/shovill
+++ b/bin/shovill
@@ -39,7 +39,7 @@
'pigz' => 'pigz --version 2>&1',
# 'mash' => 'mash --version 2>&1',
'kmc' => 'kmc -h 2>&1 | grep KMC',
- 'trimmomatic' => 'trimmomatic -version 2>&1 | grep -v _JAVA',
+ 'TrimmomaticPE' => 'TrimmomaticPE -version 2>&1 | grep -v _JAVA',
'lighter' => 'lighter -v 2>&1',
'flash' => 'flash --version 2>&1 | grep FLASH',
'spades.py' => 'spades.py --version 2>&1',
@@ -183,9 +183,9 @@
my $TRIMOPT = "ILLUMINACLIP:$ADAPTERS:1:30:11 LEADING:$MIN_BQ TRAILING:$MIN_BQ MINLEN:30 TOPHRED33";
msg("Trimming reads");
run_cmd(
- "trimmomatic PE -threads $cpus -phred33".
+ "TrimmomaticPE -threads $cpus -phred33".
" \Q$R1\E \Q$R2\E R1.fq.gz /dev/null R2.fq.gz /dev/null $TRIMOPT",
- "trimmomatic"
+ "TrimmomaticPE"
);
}
else {
|
