Programmatically save a file to Drupal from your local file system.

create_file.php

/**
 * Saves a file on your local file system you want to copy to Drupal default files directory.
 * This assumes you have bootstrapped Drupal.
 * Originally written to be invoked within a Behat context.
 */
use Drupal\file\Entity\File;

$file = File::create([
  'uid' => 1
  ]);
$file->setFilename("image-fact.jpg");
$file->setPermanent();
$file->setFileUri(rtrim(realpath("/var/www/backup/files"), DIRECTORY_SEPARATOR).DIRECTORY_SEPARATOR.$file->getFilename());
$file->set('langcode', $file->language()->getId());
$file->setChangedTime(time());
$dest = file_build_uri(drupal_basename($file->GetFileUri()));
$result = file_copy($file, $dest, FILE_EXISTS_REPLACE);


/*************************
 * REMOTE VERSION
 * This one helps you copy a file from a remote source to the local system, perhaps during a migrate.module migration.
 *************************/

use Drupal\file\Entity\File;

$this->fileSystem = \Drupal::service('file_system');

/**
 * Save the file data we retreived from external URL
 *
 * @param string $url
 * The image url to fetch.
 *
 * @return \Drupal\file\Entity\File
 */
function saveFile($url) {
    $source = $url;
    $basename = $this->fileSystem->basename($url);
    $temp_destination = 'temporary://' . $basename;
    $destination = $this->configuration['destination_path'] . $basename;

    $dir = $this->getDirectory($destination);
    if (!file_prepare_directory($dir, FILE_CREATE_DIRECTORY | FILE_MODIFY_PERMISSIONS)) {
      throw new Exception("Could not create or write to directory '$dir'");
    }

    if (@copy($source, $temp_destination)) {
      $this->file->setFilename($basename);
      $this->file->setFileUri($temp_destination);
      $this->file->setChangedTime(time());

      return file_copy($this->file, $destination, FILE_EXISTS_REPLACE);
    }
  }

/**
 * Returns the directory component of a URI or path.
 * Copied from migrate_plus module.
 *
 * For URIs like public://foo.txt, the full physical path of public://
 * will be returned, since a scheme by itself will trip up certain file
 * API functions (such as file_prepare_directory()).
 *
 * @param string $uri
 *   The URI or path.
 *
 * @return string|false
 *   The directory component of the path or URI, or FALSE if it could not
 *   be determined.
 */
function getDirectory($uri) {
  $dir = $this->fileSystem->dirname($uri);
  if (substr($dir, -3) == '://') {
    return $this->fileSystem->realpath($dir);
  }
  return $dir;
}