<?php

$collection = $this->productCollectionFactory->create();
$collection->setVisibility($this->catalogProductVisibility->getVisibleInCatalogIds());
$collection = $this->_addProductAttributesAndPrices($collection);

return $collection;

$collection = $this->productCollectionFactory->create();
$collection->setVisibility($this->catalogProductVisibility->getVisibleInCatalogIds());
$collection = $this->_addProductAttributesAndPrices($collection);
$this->stockFilter->addInStockFilterToCollection($collection);

protected $_linkFactory;

public function __construct(
    MagentoCatalogModelProductLinkFactory $linkFactory
) {
    $this->_linkFactory = $linkFactory;
}

$collection = $this->_linkFactory->create()
        ->getProductCollection()->addAttributeToSelect('*')
        ->addAttributeToFilter(
            'status', array('eq' => MagentoCatalogModelProductAttributeSourceStatus::STATUS_ENABLED)
        )
    ;

    $collection->joinField(
        'qty', 'cataloginventory_stock_item', 'qty', 'product_id=entity_id', '{{table}}.stock_id=1', 'left'
    );

/**
 * @var MagentoCatalogInventoryHelperStock
 */
protected $_stockFilter;

public function __construct(
    .....
     MagentoCatalogInventoryHelperStock $stockFilter
    .....
) {
     $this->_stockFilter = $stockFilter;
}

public function getProducts(){
..........
 $this->_stockFilter->addInStockFilterToCollection($collection);
..........
}

addInStockFilterToCollection($collection)

addIsInStockFilterToCollection($collection)

/**
     * @param MagentoCatalogModelResourceModelProductCollection $collection
     * @param bool $isFilterInStock
     * @return MagentoCatalogModelResourceModelProductCollection $collection
     */
    public function addStockDataToCollection($collection, $isFilterInStock)
    {
        $websiteId = $this->getStockConfiguration()->getDefaultScopeId();
        $joinCondition = $this->getConnection()->quoteInto(
            'e.entity_id = stock_status_index.product_id' . ' AND stock_status_index.website_id = ?',
            $websiteId
        );

        $joinCondition .= $this->getConnection()->quoteInto(
            ' AND stock_status_index.stock_id = ?',
            Stock::DEFAULT_STOCK_ID
        );
        $method = $isFilterInStock ? 'join' : 'joinLeft';
        $collection->getSelect()->$method(
            ['stock_status_index' => $this->getMainTable()],
            $joinCondition,
            ['is_salable' => 'stock_status']
        );

        if ($isFilterInStock) {
            $collection->getSelect()->where(
                'stock_status_index.stock_status = ?',
                StockStatus::STATUS_IN_STOCK
            );
        }
        return $collection;
    }