Ensure output files are emitted during incomplete runs

[jscgh]

Description of feature

Intermittently, files will not be moved to the output folder when a multi-run job fails. This leads to outputs being stuck in the work directory.

Will need to investigate using the publish vs out features available in the latest Nextflow version to ensure that module outputs are always emitted even if a job fails.

[keiran-rowell-unsw]

This has recently been causing issues for me when I was trying to run timings for increasingly large proteins.

I'll look into adding publishDir so we at least get something for a 'set-and-forget' run