old_contents: # -*- coding: utf-8 -*-
  
  """
  Copyright [2009-2021] EMBL-European Bioinformatics Institute
  Licensed under the Apache License, Version 2.0 (the "License");
  you may not use this file except in compliance with the License.
  You may obtain a copy of the License at
  http://www.apache.org/licenses/LICENSE-2.0
  Unless required by applicable law or agreed to in writing, software
  distributed under the License is distributed on an "AS IS" BASIS,
  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  See the License for the specific language governing permissions and
  limitations under the License.
  """
  
  from pathlib import Path
  
  import click
  
  from rnacentral_pipeline.writers import EntryWriter
  from rnacentral_pipeline.databases.hgnc import parser
  
  @click.group('hgnc')
  def cli():
      """
      Commands for HGNC data.
      """
  
  
  @cli.command('map')
  @click.argument('filename', type=click.Path())
  @click.argument(
      "output",
      default=".",
      type=click.Path(writable=True, dir_okay=True, file_okay=False,),
  )
  def process_hgnc(filename, output):
      """
      Process the raw HGNC file into importable CSV files
      """
      entries = parser.parse(Path(filename))
      writer = EntryWriter(output)
      writer.write(entries)
  
new_contents: # -*- coding: utf-8 -*-
  
  """
  Copyright [2009-2021] EMBL-European Bioinformatics Institute
  Licensed under the Apache License, Version 2.0 (the "License");
  you may not use this file except in compliance with the License.
  You may obtain a copy of the License at
  http://www.apache.org/licenses/LICENSE-2.0
  Unless required by applicable law or agreed to in writing, software
  distributed under the License is distributed on an "AS IS" BASIS,
  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  See the License for the specific language governing permissions and
  limitations under the License.
  """
  
  from pathlib import Path
  
  import click
  
  from rnacentral_pipeline.writers import EntryWriter
  from rnacentral_pipeline.databases.hgnc import parser
  
  
  @click.group('hgnc')
  def cli():
      """
      Commands for HGNC data.
      """
  
  
  @cli.command('map')
  @click.option('--db-url', envvar='PGDATABASE')
  @click.argument('filename', type=click.Path())
  @click.argument(
      "output",
      default=".",
      type=click.Path(writable=True, dir_okay=True, file_okay=False,),
  )
  def process_hgnc(filename, output, db_url=None):
      """
      Process the raw HGNC file into importable CSV files
      """
      entries = parser.parse(Path(filename), db_url)
      writer = EntryWriter(output)
      writer.write(entries)
  
subject: Update CLI code