Control of output file location/names

[paulaberry]

I would like to be able to specify where/with what prefixes output files should go - right now my workflow involves copying an entire BeadChip sequencing directory from separate sequencing data storage where we do not have write permissions (taking up most of my local storage), running methylprep/-check/-ize CLI, then running a bash script to delete all of the copied files and pre-pend the directory structure onto the output files and move them into the appropriate analysis directory. I have looked through the documentation but have not found anywhere to specify output path for results - is there one? If not, could there be in the future?

[notmaurox]

Hi - Have you tried constructing a work directory with symbolic links to your idats and running on that directory?