Task * MergeFastqWorker::tick() {
while (inputUrlPort->hasMessage()) {
const QString url = takeUrl();
CHECK(!url.isEmpty(), NULL);
inputUrls.append(url);
}
if (!inputUrlPort->isEnded()) {
return NULL;
}
if(!inputUrls.isEmpty()){
const QString outputDir = FileAndDirectoryUtils::createWorkingDir(inputUrls.first(), getValue<int>(OUT_MODE_ID), getValue<QString>(CUSTOM_DIR_ID), context->workingDir());
BaseNGSSetting setting;
setting.outDir = outputDir;
setting.outName = getTargetName(inputUrls.first(), outputDir);
setting.inputUrl = inputUrls.first();
setting.customParameters = getCustomParameters();
setting.listeners = createLogListeners();
Task *t = getTask(setting);
connect(new TaskSignalMapper(t), SIGNAL(si_taskFinished(Task*)), SLOT(sl_taskFinished(Task*)));
inputUrls.clear();;
return t;
}
if (inputUrlPort->isEnded()) {
setDone();
outputUrlPort->setEnded();
}
return NULL;
}
Task * SortBamWorker::tick() {
if (inputUrlPort->hasMessage()) {
const QString url = takeUrl();
CHECK(!url.isEmpty(), NULL);
const QString detectedFormat = FileAndDirectoryUtils::detectFormat(url);
if(detectedFormat.isEmpty()){
coreLog.info(tr("Unknown file format: ") + url);
return NULL;
}
if(detectedFormat == BaseDocumentFormats::BAM){
const QString outputDir = FileAndDirectoryUtils::createWorkingDir(url, getValue<int>(OUT_MODE_ID), getValue<QString>(CUSTOM_DIR_ID), context->workingDir());
BamSortSetting setting;
setting.outDir = outputDir;
setting.outName = getTargetName(url, outputDir);
setting.inputUrl = url;
setting.index = getValue<bool>(INDEX_ID);
Task *t = new SamtoolsSortTask(setting);
connect(new TaskSignalMapper(t), SIGNAL(si_taskFinished(Task*)), SLOT(sl_taskFinished(Task*)));
return t;
}
}
if (inputUrlPort->isEnded()) {
setDone();
outputUrlPort->setEnded();
}
return NULL;
}
Task * RmdupBamWorker::tick() {
if (inputUrlPort->hasMessage()) {
const QString url = takeUrl();
CHECK(!url.isEmpty(), NULL);
const QString detectedFormat = FileAndDirectoryUtils::detectFormat(url);
if(detectedFormat.isEmpty()){
coreLog.info(tr("Unknown file format: ") + url);
return NULL;
}
if(detectedFormat == BaseDocumentFormats::BAM){
const QString outputDir = FileAndDirectoryUtils::createWorkingDir(url, getValue<int>(OUT_MODE_ID), getValue<QString>(CUSTOM_DIR_ID), context->workingDir());
BamRmdupSetting setting;
setting.outDir = outputDir;
setting.outName = getTargetName(url, outputDir);
setting.inputUrl = url;
setting.removeSingleEnd = getValue<bool>(REMOVE_SINGLE_END_ID);
setting.treatReads = getValue<bool>(TREAT_READS_ID);
SamtoolsRmdupTask *t = new SamtoolsRmdupTask(setting);
t->addListeners(createLogListeners());
connect(new TaskSignalMapper(t), SIGNAL(si_taskFinished(Task*)), SLOT(sl_taskFinished(Task*)));
return t;
}
}
if (inputUrlPort->isEnded()) {
setDone();
outputUrlPort->setEnded();
}
return NULL;
}
Task * SnpEffWorker::tick() {
if (inputUrlPort->hasMessage()) {
const QString url = takeUrl();
CHECK(!url.isEmpty(), NULL);
QString outputDir = FileAndDirectoryUtils::createWorkingDir(url, getValue<int>(OUT_MODE_ID), getValue<QString>(CUSTOM_DIR_ID), context->workingDir());
U2OpStatusImpl os;
outputDir = GUrlUtils::createDirectory(outputDir + SnpEffWorker::BASE_SNPEFF_SUBDIR, "_", os);
SnpEffSetting setting;
setting.inputUrl = url;
setting.outDir = outputDir;
setting.inFormat = getValue<QString>(INPUT_FORMAT);
setting.outFormat = getValue<QString>(OUTPUT_FORMAT);
setting.genome = getValue<QString>(GENOME);
setting.updownLength = getValue<QString>(UPDOWN_LENGTH);
setting.canon = getValue<bool>(CANON);
setting.hgvs = getValue<bool>(HGVS);
setting.lof = getValue<bool>(LOF);
setting.motif = getValue<bool>(MOTIF);
SnpEffTask *t = new SnpEffTask (setting);
connect(new TaskSignalMapper(t), SIGNAL(si_taskFinished(Task*)), SLOT(sl_taskFinished(Task*)));
QList<ExternalToolListener *> listeners = createLogListeners();
listeners[0]->setLogProcessor(new SnpEffLogProcessor(monitor(), getActorId()));
t->addListeners(listeners);
return t;
}
if (inputUrlPort->isEnded()) {
setDone();
outputUrlPort->setEnded();
}
return NULL;
}