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I can confirm this seems to be happening on my side as well when using an input function designed to return a path of the form: /storage/users/user/Reference Genomes/GRCh38.fa.gz, I end up getting a debug message stating :
Missing files after 5 seconds:
/storage/users/user/Reference
Genomes/GRCh38.fa.gz
I have tracked it back to this stack overflow submission, where it was pointed out by @Manavalan Gajapathy that you can use quotation marks in shell scripts to honour the whitespace in the command itself. With that in mind, this behaviour would indicate that the fault lies in some kind of check-up script that is run by snakemake to 'watch' for the output files?
Just a quick update. I changed my filename from Reference Genome to Reference_Genome and viola! Worked like a bomb. Definitely seems like something to do with how Snakemake handles file waiting.
As a side note, I did try to dig around the codebase myself, but despite getting pretty far along, I cant seem to find any functions relating to the wait_for_files group of functions called on inputs spesifically, much fewer inputs from function-based inputs as is my case (Though between @fneum and I's issue, it would indicate it's not an issue with function-based inputs specifically, just inputs in general?)
Snakemake version
6.5.1
(did not yet track down the version where this first occurred, but somewhere after 6.1.0)
Describe the bug
Only when using
snakemake --cluster ...
, input filenames are split at whitespaces resulting in missing files.Possibly related to #1007?
Logs
Minimal example
Additional context
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