feat: Allow outputting of rendered yte config in Datavzrd wrapper (#3123

)

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`snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html).

While the contributions guidelines are more extensive, please
particularly ensure that:
* [ ] `test.py` was updated to call any added or updated example rules
in a `Snakefile`
* [ ] `input:` and `output:` file paths in the rules can be chosen
arbitrarily
* [ ] wherever possible, command line arguments are inferred and set
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* [ ] temporary files are either written to a unique hidden folder in
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<!-- This is an auto-generated comment: release notes by coderabbit.ai
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## Summary by CodeRabbit


- **New Features**
- Added an optional output configuration file in YAML format for
enhanced tracking of pipeline parameters and settings.
- Implemented functionality to save processed data to a specified output
configuration path, improving workflow management.
- Enhanced metadata in the configuration file with additional context
regarding the output structure and location.

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

---------

Co-authored-by: Johannes Köster <[email protected]>

utils/datavzrd/meta.yaml

@@ -6,5 +6,7 @@ description: |
   Any files specified in the configuration file have to be also specified as additional input files in the
   datavzrd rule.
 url: https://github.com/datavzrd/datavzrd
+output:
+- config: Path to the rendered yte config
 authors:
   - Felix Mölder

utils/datavzrd/test/Snakefile

@@ -21,6 +21,8 @@ rule datavzrd:
             # see https://snakemake.readthedocs.io/en/stable/snakefiles/reporting.html
             # for additional options like caption, categories and labels
         ),
+        # optionally output the rendered config
+        config = "resources/datavzrd/{sample}.rendered_config.yaml"
     log:
         "logs/datavzrd_report/{sample}.log",
     wrapper:

utils/datavzrd/wrapper.py

@@ -6,6 +6,7 @@
 import tempfile
 from yte import process_yaml
 from snakemake.shell import shell
+import shutil
 
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
@@ -27,4 +28,6 @@
     )
     processed.flush()
 
+    if snakemake.output.config:
+        shutil.copy(processed.name, snakemake.output.config)
     shell("datavzrd {processed.name} {extra} --output {snakemake.output[0]} {log}")