Changing the logic for 'input.check' files creation

[cosimolupo]

As a preparatory step for CWL integration into Cobrawap as an alternative workflow manager, this PR proposes a different logic for the creation of input.check files.
The old method consisted in check_input.py blocks just reading neo files and checking for their consistency, producing no output files. Snakemake rule check_input was then explicitly asked for the creation of such files, via the shell command touch.
In the new approach, it is the check_input.py block itself that creates an empty output file named input.check, at the end of consistency checks and hence only after their successful ending. --output command-line argument is then added to such blocks. Snakemake rule check_input is changed accordingly, removing the shell command and adding the output field typically used for standard I/O blocks.
This new approach greatly helps in the I/O binding between steps in CWL workflows.