Shared results-folder between different pipeline runs?

[asp8200]

Description of feature

It is possible to run Sarek repeatedly for the same sample or different samples using the same output-folder (results-folder), and some users do run Sarek like that.

Currently there are a number of issues with reusing the results-folder.

1. The multiqc-data gets overwritten,
2. joint-germline-data gets overwritten,
3. csv/variantcalled.csv gets overwritten, (there is probably more files that get overwritten)
4. if starting more pipelines at the exact same time, then different pipelines may construct pipeline-info-files with exactly the same name. (Tower actually did this at DNGC; bug reported to Rob Syme and Harshil Patel.)
5. Using the same results-folder for different pipeline-runs makes it very difficult to subsequently, say, find and delete all files from some particular pipeline-run.

Should we try to solve those issue?

Perhaps we just want to advise against using the same results-folder for different pipeline-runs?

N.B. What about work-folders? On re-runs (-resume) one, of course, wants to use the same work-folder, but what about work-folders for pipeline-runs of different samples? I see no reason that they should share work-folders. (I know that the subfolders with the hash-strings make any clashes/conflicts between pipelines sharing the same work-folder very unlikely, but still?)