search

rotary-genomics / rotary

Assembly/annotation workflow for Nanopore-based microbial genome data containing circular DNA elements
BSD 3-Clause "New" or "Revised" License
2 stars 1 forks source link

Add flag to keep final QC read files #129

Closed jmtsuji closed 7 months ago

jmtsuji commented 7 months ago

Similar to #119 , I often find it helpful to keep the final QC files for short/long reads so that I can check the quality of the assembly, redo read mapping, and so on. Like #119 , I am interested in adding a flag to the config file so that the final long/short read QC files are not temp() -- what do you think @LeeBergstrand ?

LeeBergstrand commented 7 months ago

@jmtsuji That could work. I would be open to that. We might want to mention in the docs that they can run --no-temp to keep all the intermediary files. I think that a config flag for this is OK.

LeeBergstrand commented 7 months ago

Addressed in https://github.com/rotary-genomics/rotary/pull/130