Software version not collected

[kristinebilgrav]

Need

As a developer,
I want the software versions to be collected,
so that we can properly test if there are software changes for a pipeline run.

Bug identified in #26.

Acceptance criteria

• All software versions are published to oncorefiner_software_mqc_versions.yml
• The versions topic channel is used to collect software versions.
  • All nf-core modules are updated to implement latest nf-core changes that use the versions topic channel.

[fellen31]

• populating ch_versions in workflows/oncorefiner.nf

Note that all nf-core modules are being switched to topics channels, where you no longer need to populate ch_versions. It might be a better strategy to instead update all modules, rather than for you to have to populate ch_versions and then remove it again pretty soon.

However, it looks like the part where the versions topic channel is collected perhaps got lost when updating the template in oncorefiner? Compare for example with raredisease: https://github.com/nf-core/raredisease/blob/6a63ade4631b999b1bd0c54d65fda891ffb59907/workflows/raredisease.nf#L804-L837

[beatrizsavinhas]

Exactly what I was thinking @fellen31! I'll update the acceptance criteria to require topic channels instead!