Only the ZARP execution directory and the run directory for every given workflow are bind mounted to Singularity. If input files do not reside in any of these directories or their subdirectories, input files will not be found.
Solution
Pass locations of all input files to --singularity-args '--bind PATH_1,PATH_2', for example by interfacing a parameter that takes a list of paths inSnakemakeExecutor` constructor. Calling modules can then parse all required paths from the record object and pass them along.
Problem
Only the ZARP execution directory and the run directory for every given workflow are bind mounted to Singularity. If input files do not reside in any of these directories or their subdirectories, input files will not be found.
Solution
Pass locations of all input files to
--singularity-args '--bind PATH_1,PATH_2', for example by interfacing a parameter that takes a list of paths inSnakemakeExecutor` constructor. Calling modules can then parse all required paths from the record object and pass them along.