Add meta to all modules

[nschcolnicov]

After converting some of the modules to nf-core we had to add meta to the input/output channels.
Some of the modules that weren't migrated don't have meta, which makes us have to filter items from input and output channels.
We should modify all of the modules that are affected by this to include meta

Once these PRs get merged:
#114
nf-core/modules#7108
nf-core/modules#7100

FYI @alanmmobbs93

[nschcolnicov]

@alanmmobbs93 already taking care of this in #117