How to manually setup flake8 as PyCharm external tool

File / Settings / Tools / External Tools / Add
Name: Flake8
Program: $PyInterpreterDirectory$/python
Parameters: -m flake8 --max-complexity 10 --ignore E501,C812,I001,I003,I004 $FilePath$
Working directory: $ProjectFileDir$

Output Filters / Add
Name: Filter 1
Regular expression to match output:
$FILE_PATH$\:$LINE$\:$COLUMN$\:.*

To check source with flake8:
Tools / External Tools / Flake8

Can be used with single files as well as with directories, recursively.