I have a very particular use case. I have a very simple script that moves directories from one part of the file system to another (they are mostly sequencing runs) and updates a database, I put that as a nextflow pipeline and my plan was to use that on the seqera platform to move data (it’s a long story about why we need to do that). I can do this using a conda environment. However, if I try to use a container then the filesystem areas that I need are not bound by default. How can I do that? Do you have a suggestion for this use case? My sample sheet would be something like:
source_directory, target_directory, principal_investigator
I specify the above attributes as “vals” as this really involves moving things around the file system and it seems different than what I usually do (start with fastqs for example, and then doing a chain of commands to them, which would end with an output). Do you have any particular suggestions for this?