Huh, must have made a mistake and run both runs with the same outdir.

Yes, it is good practice to start each pipeline run (for a separate experiment) from a separate directory, so that the logs (

.nextflow.log

) and histories (in

.nextflow

) don't get crossed (this helps if you need to use

-resume

). If you have specified a relative path for the results directory, this pratice will also keep those separate (and if you use the default for the work directory,

./work

, those will be separate as well, so if you wipe one, it won't affect the other). P.S.: Please use "Reply in thread" to keep replies/answers together and help the post stay organized.

I should have probably read the nextflow documentation before running the pipeline, in hindsight given all the problems I had with this, the idea to separate the runs completely would be probably a better one since the nextflow logs and history and a little bit confusing.