Mbarba/brc mode

[MatBarba]

Clean up brc_mode usage:

• define as 0 by default in all pipelines
• remove from scripts where it is not used
• use params.brc_mode universally
• add some basic pipeline tests

[JAlvarezJarreta]

Looks great, couple of minor changes.

Two comments (not affecting the approval in any way):

• I fear how this is going to be merged with PR#173 (there are places that have been changed in both)
• I'm wondering if there is something similar than the parametrize in pytest for the Nextflow tests to avoid reflecting information such as _brc_mode_of in the name...

[MatBarba]

Looks great, couple of minor changes.

Two comments (not affecting the approval in any way):

* I fear how this is going to be merged with PR#173 (there are places that have been changed in both)

Rebase/merges make it pretty easy to resolve conflicts along the way. We just need to make sure that the tests work in the end.

* I'm wondering if there is something similar than the parametrize in pytest for the Nextflow tests to avoid reflecting information such as `_brc_mode_of` in the name...

Some of the files contents should actually differ, so we do need that distinction. I don't intend to add other variations though.