Get Software Versions process not run if DamageProfiler skipped

[jfy133]

Describe the bug
If you do not have damageprofiler running in your run (with --skip_deduplication), get_software_versions process is not executed.

To Reproduce
See above

Expected behaviour
get_software_versions always run with whatever tools are accessible.

Additional context
Partly due to the awkward way of getting the DamageProfiler versions (i.e. from the log file), so must be given to the process as an input channel.

[jfy133]

This is also an issue for the GATK_UG branch

[jfy133]

Possible solution?

https://github.com/nextflow-io/patterns/blob/master/docs/optional-input.adoc

[apeltzer]

Yeah, the problem is that the DamageProfiler tool doesn't write out a JSON file unfortunately with the information that we'd need at the moment. Since v0.4.6 it can do that, but MultiQC v1.8 isn't out (yet) that could parse this information automatically from the JSON that DamageProfiler nowadays creates automatically.

=> Once we have MultiQC v1.8, this will be gone immediately and we can also the same approach than with other tools ...

[jfy133]

Coming this afternoon from @aidaanva

[jfy133]

Done in #292