Post DeDup BAM files not published to correct publishDir

[jfy133]

Describe the bug
When running 2.0.7dev, I noticed that the post-DeDup BAM files are not found in the correct final output DeDup directory.

The BAM files sit directly in dedup/ rather than the specific sample directory that contains the .log and
.hist files
To Reproduce
Run the pipeline with DeDup on.

Expected behavior

The post-DeDup bam to be published under: deuplication/dedup/<SAMPLE>.filtered/<BAM_FILE>

[apeltzer]

Ah but that was actually intentional by me - to keep the directory a bit cleaner, having the hist and log files only accessible in subdirs makes it a bit less crowded if running many samples at once. Should I still change it?

[jfy133]

Mm ok. I personally would find it confusing (as I did), because if I see a directory for a sample I expect everything related to that sample to be in the same place. I actually originally thought the bams weren't published, because when I checked on my file browser all I saw were directories. As I had so many samples I scrolled once or twice and didn't see anything else (should've kept scrolling ;)) but still. IMO organisation wise I think you should only have to look in one place for all output of all samples so it is consistent. If it's in sample specific directory then everything is that. If all samples are in a common directory, then everything related to all the samples should also be there.

…

--- Sent my from my mobile

On Fri, 29 Mar 2019, 15:33 Alexander Peltzer, ***@***.***> wrote: Ah but that was actually intentional by me - to keep the directory a bit cleaner, having the hist and log files only accessible in subdirs makes it a bit less crowded if running many samples at once. Should I still change it? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#183 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ARHmTzA75gSzwSGOTi8HQmXBwF9x9JFYks5vbiQigaJpZM4cR7Br> .