Allow direct call of quality checks

[RubenChM]

• Each should has its own flag to be call individually from the workflow for the user to check problems before running the whole workflow/keep running a simulation.
• Divide input checker in different functions each with its own doc-string so it can be used to update the documentation
• Add outputs the the data checks so the user can explore by himself when a check is failing, e.g., if intrajrity fails, save the rmsd check.