1 /**
2 * UGENE - Integrated Bioinformatics Tools.
3 * Copyright (C) 2008-2021 UniPro <ugene@unipro.ru>
4 * http://ugene.net
5 *
6 * This program is free software; you can redistribute it and/or
7 * modify it under the terms of the GNU General Public License
8 * as published by the Free Software Foundation; either version 2
9 * of the License, or (at your option) any later version.
10 *
11 * This program is distributed in the hope that it will be useful,
12 * but WITHOUT ANY WARRANTY; without even the implied warranty of
13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14 * GNU General Public License for more details.
15 *
16 * You should have received a copy of the GNU General Public License
17 * along with this program; if not, write to the Free Software
18 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
19 * MA 02110-1301, USA.
20 */
21
22 #include "TrimmomaticTask.h"
23
24 #include <U2Core/Counter.h>
25 #include <U2Core/GUrlUtils.h>
26 #include <U2Core/U2SafePoints.h>
27
28 #include "TrimmomaticLogParser.h"
29 #include "TrimmomaticSupport.h"
30
31 namespace U2 {
32
33 const QString TrimmomaticTaskSettings::SINGLE_END = "single-end";
34 const QString TrimmomaticTaskSettings::PAIRED_END = "paired-end";
35
TrimmomaticTaskSettings()36 TrimmomaticTaskSettings::TrimmomaticTaskSettings()
37 : pairedReadsInput(false),
38 generateLog(false),
39 numberOfThreads(1) {
40 }
41
TrimmomaticTask(const TrimmomaticTaskSettings & settings)42 TrimmomaticTask::TrimmomaticTask(const TrimmomaticTaskSettings &settings)
43 : ExternalToolSupportTask(tr("Improve reads with Trimmomatic"), TaskFlags_NR_FOSE_COSC),
44 settings(settings),
45 trimmomaticToolRunTask(nullptr) {
46 GCOUNTER(cvar, "TrimmomaticTask");
47
48 if (settings.pairedReadsInput) {
49 SAFE_POINT_EXT(!settings.pairedOutputUrl1.isEmpty() && !settings.pairedOutputUrl2.isEmpty() &&
50 !settings.unpairedOutputUrl1.isEmpty() && !settings.unpairedOutputUrl2.isEmpty(),
51 setError("At least one of the four output files is not set!"), );
52 } else {
53 SAFE_POINT_EXT(!settings.seOutputUrl.isEmpty(), setError("Output file is not set!"), );
54 }
55
56 SAFE_POINT_EXT(!(settings.generateLog && settings.logUrl.isEmpty()), setError("Log file is not set!"), );
57 }
58
prepare()59 void TrimmomaticTask::prepare() {
60 trimmomaticToolRunTask = new ExternalToolRunTask(TrimmomaticSupport::ET_TRIMMOMATIC_ID, getArguments(), new TrimmomaticLogParser(), settings.workingDirectory);
61 setListenerForTask(trimmomaticToolRunTask);
62 addSubTask(trimmomaticToolRunTask);
63 }
64
getArguments()65 QStringList TrimmomaticTask::getArguments() {
66 QStringList arguments;
67
68 if (!settings.pairedReadsInput) {
69 arguments << "SE";
70 } else {
71 arguments << "PE";
72 }
73
74 arguments << "-threads" << QString::number(settings.numberOfThreads);
75
76 if (settings.generateLog) {
77 arguments << "-trimlog" << settings.logUrl;
78 GUrlUtils::prepareFileLocation(settings.logUrl, stateInfo);
79 }
80
81 if (!settings.pairedReadsInput) {
82 arguments << settings.inputUrl1;
83 arguments << settings.seOutputUrl;
84 GUrlUtils::prepareFileLocation(settings.seOutputUrl, stateInfo);
85 } else {
86 arguments << settings.inputUrl1;
87 arguments << settings.inputUrl2;
88 arguments << settings.pairedOutputUrl1;
89 arguments << settings.unpairedOutputUrl1;
90 arguments << settings.pairedOutputUrl2;
91 arguments << settings.unpairedOutputUrl2;
92 GUrlUtils::prepareFileLocation(settings.pairedOutputUrl1, stateInfo);
93 GUrlUtils::prepareFileLocation(settings.pairedOutputUrl2, stateInfo);
94 GUrlUtils::prepareFileLocation(settings.unpairedOutputUrl1, stateInfo);
95 GUrlUtils::prepareFileLocation(settings.unpairedOutputUrl2, stateInfo);
96 }
97
98 foreach (QString step, settings.trimmingSteps) {
99 step.remove('\'');
100 arguments << step;
101 }
102
103 return arguments;
104 }
105
getInputUrl1() const106 const QString &TrimmomaticTask::getInputUrl1() const {
107 return settings.inputUrl1;
108 }
109
getSeOutputUrl() const110 const QString &TrimmomaticTask::getSeOutputUrl() const {
111 return settings.seOutputUrl;
112 }
113
getPairedOutputUrl1() const114 const QString &TrimmomaticTask::getPairedOutputUrl1() const {
115 return settings.pairedOutputUrl1;
116 }
117
getPairedOutputUrl2() const118 const QString &TrimmomaticTask::getPairedOutputUrl2() const {
119 return settings.pairedOutputUrl2;
120 }
121
getUnpairedOutputUrl1() const122 const QString &TrimmomaticTask::getUnpairedOutputUrl1() const {
123 return settings.unpairedOutputUrl1;
124 }
125
getUnpairedOutputUrl2() const126 const QString &TrimmomaticTask::getUnpairedOutputUrl2() const {
127 return settings.unpairedOutputUrl2;
128 }
129
getLogUrl() const130 const QString &TrimmomaticTask::getLogUrl() const {
131 return settings.logUrl;
132 }
133
134 } // namespace U2
135