🤖 I have created a release *beep* *boop*
---


##
[9.13.5](v9.13.4...v9.13.5)
(2025-11-04)


### Bug Fixes

* cache wrapper files and wait for them in case of shared filesystem for
sources ([#3809](#3809))
([498fff7](498fff7))
* correctly handle meta-wrapper tag replacement depending on the used
snakemake-wrapper release
([#3826](#3826))
([8d46a4a](8d46a4a))
* ensure that flags are properly considered for input files before
applying path modifiers (i.e. default storage providers)
([#3813](#3813))
([d3bfe32](d3bfe32))
* ensure that tokens are not leaked when paths or uris of source files
are logged ([#3821](#3821))
([a217e50](a217e50))
* print secs as numeric in jsonl benchmark format
([#3814](#3814))
([395a5e6](395a5e6))
* revert breaking change in 9.11.9 disallowing empty input files even
when unused
([#3810](#3810))
([83c05cc](83c05cc))
* shorten report ids (thus dir names) in order to avoid issues with path
length on windows
([#3822](#3822))
([b24d971](b24d971))

---
This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).

…ven when unused (snakemake#3810)

Reverts a breaking change introduced in version 9.11.9 where all input
files were required to be non-empty, even if they were not actually used
by a rule.

snakemake#3801 suggested that it would be acceptable to raise an error for this
in the future, as long as there is a deprecation warning period or it
comes with a major version bump, and a warning sounds good for now.

Thanks @corneliusroemer for pointing this out, and apologies for my
earlier overzealous modification.


### QC
<!-- Make sure that you can tick the boxes below. -->

* [ ] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [ ] The documentation (`docs/`) is updated to reflect the changes or
this is not necessary (e.g. if the change does neither modify the
language nor the behavior or functionalities of Snakemake).


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

* **Bug Fixes**
* Improved handling of empty file paths by providing informative
guidance instead of raising an error. The system now logs a warning
message directing users to use an empty list ([]) to indicate no files,
making workflows more forgiving and easier to debug.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

🤖 I have created a release *beep* *boop*
---


##
[9.13.5](snakemake/snakemake@v9.13.4...v9.13.5)
(2025-11-04)


### Bug Fixes

* cache wrapper files and wait for them in case of shared filesystem for
sources ([snakemake#3809](snakemake#3809))
([498fff7](snakemake@498fff7))
* correctly handle meta-wrapper tag replacement depending on the used
snakemake-wrapper release
([snakemake#3826](snakemake#3826))
([8d46a4a](snakemake@8d46a4a))
* ensure that flags are properly considered for input files before
applying path modifiers (i.e. default storage providers)
([snakemake#3813](snakemake#3813))
([d3bfe32](snakemake@d3bfe32))
* ensure that tokens are not leaked when paths or uris of source files
are logged ([snakemake#3821](snakemake#3821))
([a217e50](snakemake@a217e50))
* print secs as numeric in jsonl benchmark format
([snakemake#3814](snakemake#3814))
([395a5e6](snakemake@395a5e6))
* revert breaking change in 9.11.9 disallowing empty input files even
when unused
([snakemake#3810](snakemake#3810))
([83c05cc](snakemake@83c05cc))
* shorten report ids (thus dir names) in order to avoid issues with path
length on windows
([snakemake#3822](snakemake#3822))
([b24d971](snakemake@b24d971))

---
This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).