Only a single dedup.log file is exported to final deduplication/dedup directory

[jfy133]

Describe the bug
Presumably due to having the same name, only a single dedup.log file is present in the deduplication/dedup output directory. Note that the .hist files are correctly there for every sample. Just the .log is not.

To Reproduce
Run a pipeline (-r dev) with DeDup included.

Expected behavior
A dedup.log file is presented for every sample

[apeltzer]

Ah that should be an easy fix .... its just not yet published the file, they're all there. Never thought anybody wants them to be able to see them ;-)

[jfy133]

Yeah exactly, they are in work/* but I have a feeling when 'publishing' them to the main output directory each one overwrites the other. If that's what you mean.

Me neither, very much an edge case when trying to fix the DamageProfiler/Qualimap issue from 2.0.5, and I re-ran MultiQC. Would never have had noticed otherwise 😆

[apeltzer]

Ah its not a problem to have multiple output folders based on sample names in the $outdir folder at all, can do that 👍