Integrate subworkflows into pipeline

[suzannejin]

• Update nf-core modules #428
• Add subworkflows
• Replace the current calls to DE modules by a call to the differential subworkflow created in Create 'differential' subworkflow #341 .
• Replace the current calls to functional analysis modules by a call to the subworkflow in Create a subworkflow for functional analysis methods #384
• Make sure it reproduces the same exact results as the current pipeline

[suzannejin]

Subworkflows are ready:

• Create 'differential' subworkflow #341
• Create a subworkflow for functional analysis methods #384

Starting to work on this issue now.