Add parameter to publish more results

[hoelzer]

From a user feedback: the output is nice but if some strange sample is included that one wants to investigate further (using the BAMs, VCF, intermediate files, ...) it would be great to not have to go through all the work folder structure.

Suggestion: we could add some parameter like --publish-all that can be used to activate more publish options in the processes. Thus, one could easily use

... -resume --publish-all

to rerun and just - w/o re-calc - publish more files from the work folders. E.g. in some "intermediate data" folder or so?

That would users help to check for problems in their data.

[replikation]

• its usually just the artic stuff or?
• we could add this to publish dir vor the assembly and publish the whole thing?

[hoelzer]

yeah you are right, mainly all the ARTIC stuff.

You mean just adding this in general to publish? Many more files I guess which might be also confusing... or we just have a 09-all-artic-files folder and just publish the whole artic pipeline output into that folder in general. In case someone needs to inspect stuff