From e74be7843299478a276febfacb52825a9762500c Mon Sep 17 00:00:00 2001
From: Felix Wiegand <fxwiegand@wgdnet.de>
Date: Wed, 21 Aug 2024 10:39:10 +0200
Subject: [PATCH] feat: Allow outputting of rendered yte config in Datavzrd
 wrapper (#3123)
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### QC
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* [ ] I confirm that I have followed the [documentation for contributing
to
`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
automatically (e.g. based on file extensions in `input:` or `output:`)
* [ ] temporary files are either written to a unique hidden folder in
the working directory, or (better) stored where the Python function
`tempfile.gettempdir()` points to
* [ ] the `meta.yaml` contains a link to the documentation of the
respective tool or command under `url:`
* [ ] conda environments use a minimal amount of channels and packages,
in recommended ordering


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## 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 <johannes.koester@uni-due.de>
---
 utils/datavzrd/meta.yaml      | 2 ++
 utils/datavzrd/test/Snakefile | 2 ++
 utils/datavzrd/wrapper.py     | 3 +++
 3 files changed, 7 insertions(+)

diff --git a/utils/datavzrd/meta.yaml b/utils/datavzrd/meta.yaml
index 29f7caa14a..a9a3c6f990 100644
--- a/utils/datavzrd/meta.yaml
+++ b/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
diff --git a/utils/datavzrd/test/Snakefile b/utils/datavzrd/test/Snakefile
index 03b70eba31..6c9eaef015 100644
--- a/utils/datavzrd/test/Snakefile
+++ b/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:
diff --git a/utils/datavzrd/wrapper.py b/utils/datavzrd/wrapper.py
index d0138a287f..03dd330d97 100644
--- a/utils/datavzrd/wrapper.py
+++ b/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}")