Use when() instead
$count = Project::query()
->when($active, function ($query) {
$query->active();
})
->when($running, function($query, {
$query->where('start_date', '<=', Carbon::today());
$query->where('end_date', '>=', Carbon::today());
}, function($query) {
$query->where('start_date', '>', Carbon::today());
$query->where('end_date', '<', Carbon::today());
})->count();