fix: ensure that log and benchmark files are uploaded to storage as w…

…ell (#2545)

### Description

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### QC
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* [x] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [x] 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).

docs/getting_started/migration.rst

@@ -22,7 +22,14 @@ Snakemake 8 removes the support for four syntactical elements, which are all off
 * Support for marking output files as ``dynamic`` has been removed. You should instead use :ref:`checkpoints <snakefiles-checkpoints>`.
 * Support for the ``version`` directive has been removed. You should use the :ref:`conda <integrated_package_management>` or :ref:`container <apptainer>` integration instead.
 * Support for the ``subworkflow`` directive has been removed. You should use the :ref:`module directive <snakefiles-modules>` instead, which provides the same functionality in a more general way.
-* Support for remote providers has been removed. You should use :ref:`storage plugins <storage-support>` instead.
+* Support for remote providers has been removed. You should use :ref:`storage plugins <storage-support>` instead. 
+  Most of the old remote providers have been migrated into the new storage plugins
+  (see the `Snakemake plugin catalog <https://snakemake.github.io/snakemake-plugin-catalog>`_.).
+  Two former remote providers have been migrated into Snakemake wrappers instead, namely 
+  the NCBI and ENA remote providers, which are now replaced by the 
+  `entrez/efetch <https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/entrez/efetch.html>`_ and 
+  the `ena <https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/ena.html>`_ wrappers.
+
 
 Command line interface
 ^^^^^^^^^^^^^^^^^^^^^^

snakemake/dag.py

@@ -349,11 +349,13 @@ async def store_storage_outputs(self):
             logger.info("Storing output in storage.")
             async with asyncio.TaskGroup() as tg:
                 for job in self.needrun_jobs(exclude_finished=False):
-                    for f in job.output:
+                    benchmark = [job.benchmark] if job.benchmark else []
+                    for f in chain(job.output, job.log, benchmark):
                         if (
                             f.is_storage
                             and f
                             not in self.workflow.storage_settings.unneeded_temp_files
+                            and f.exists_local()
                         ):
                             tg.create_task(f.store_in_storage())