Update nf-core modules

[suzannejin]

The nf-core modules currently installed in the pipeline are outdated. They need to be updated.

Snapshots need to be updated too, as module behaviour might be slightly different.
For example: before, deseq2 was by default rounding some results (eg. vst file, and differential results, but not the normalized counts) to 8 digits. Not anymore now (round_digits = NULL).

[suzannejin]

Ongoing work:

• Update nf-core modules with new nftests #420

Also in:

• Integrate subworkflows into pipeline #431