Workflow restructure and optimizations

Optimize the workflow structure and unblock the processes post alignment.
Update the default reference genome and reconfigure iGenomes.conf to use on-prem S3.

What's Changed

• Feature/cram input by @matthdsm in #24
• update modules structure by @matthdsm in #27
• Feat/nfcore subwf by @matthdsm in #29
• Feat/nfcore subwf by @matthdsm in #31
• Revert "Feat/nfcore subwf" by @matthdsm in #32
• Wf restructure by @matthdsm in #33
• Feat/ugent igenomes by @matthdsm in #42
• Dev by @matthdsm in #37

Full Changelog: v1.0.1...v1.1.0