In the FileCheck rule, we call the function fileCheckFunc() to let snakemake know what missing csv files will be written. This line is doing something weird to osemosysFiles list variable being passed around, which holds the master list of all required CSVs. After this point the osemosysFiles list is no longer recognized by any input or output parameters (see images below)
A couple of points that may help to solve this issue:
Any reference to the osemosysFiles list above this line in the file works fine. This is the quick fix method implemented in pr #86. More information on how snakemake initializes and builds the workflow here
Information on how to use functions for input files here
May want to look at generalizing the workflow more with just using wildcards instead of the expand function. Not sure if this is totally feasible or even the source of the error.
https://github.com/OSeMOSYS/osemosys_global/blob/d9268a52fa9cb423a5dbccfd9beefc5d64e6f72a/src/osemosys_global/snakefile#L308
In the FileCheck rule, we call the function
fileCheckFunc()to let snakemake know what missing csv files will be written. This line is doing something weird toosemosysFileslist variable being passed around, which holds the master list of all required CSVs. After this point theosemosysFileslist is no longer recognized by any input or output parameters (see images below)A couple of points that may help to solve this issue:
osemosysFileslist above this line in the file works fine. This is the quick fix method implemented in pr #86. More information on how snakemake initializes and builds the workflow here