Drive reference data and resource file data staging through CLI option

[scwatts]

Description of feature

• currently the reference data / resource file staging feature is partial driven by the composition of the samplesheet
• specifically, only files required to analyse data in the samplesheet will be retrieved or prepared
• this approach is efficient in terms of implementation but is not particularly intuitive for users
• selection of reference data / resource files to retrieve should instead be driven by a CLI argument

[scwatts]

@luan-n-nguyen let's separate development for this enhancement in a new branch to avoid complications with the changes WiGiTS v6.0