fix: output file handling in ensembl-variation wrapper in combination…

… with remote storage or absolute output file paths (#2753)

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### QC
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* [x] I confirm that:

For all wrappers added by this PR, 

* there is a test case which covers any introduced changes,
* `input:` and `output:` file paths in the resulting rule can be changed
arbitrarily,
* either the wrapper can only use a single core, or the example rule
contains a `threads: x` statement with `x` being a reasonable default,
* rule names in the test case are in
[snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell
what the rule is about or match the tools purpose or name (e.g.,
`map_reads` for a step that maps reads),
* all `environment.yaml` specifications follow [the respective best
practices](https://stackoverflow.com/a/64594513/2352071),
* the `environment.yaml` pinning has been updated by running
`snakedeploy pin-conda-envs environment.yaml` on a linux machine,
* wherever possible, command line arguments are inferred and set
automatically (e.g. based on file extensions in `input:` or `output:`),
* all fields of the example rules in the `Snakefile`s and their entries
are explained via comments (`input:`/`output:`/`params:` etc.),
* `stderr` and/or `stdout` are logged correctly (`log:`), depending on
the wrapped tool,
* 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 (see
[here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir);
this also means that using any Python `tempfile` default behavior
works),
* the `meta.yaml` contains a link to the documentation of the respective
tool or command,
* `Snakefile`s pass the linting (`snakemake --lint`),
* `Snakefile`s are formatted with
[snakefmt](https://github.com/snakemake/snakefmt),
* Python wrapper scripts are formatted with
[black](https://black.readthedocs.io).
* Conda environments use a minimal amount of channels, in recommended
ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as
conda-forge should have highest priority and defaults channels are
usually not needed because most packages are in conda-forge nowadays).

bio/reference/ensembl-variation/wrapper.py

@@ -77,19 +77,20 @@
 try:
     gather = "curl {urls}".format(urls=" ".join(map("-O {}".format, urls)))
     workdir = os.getcwd()
+    out = os.path.abspath(snakemake.output[0])
     with tempfile.TemporaryDirectory() as tmpdir:
         if snakemake.input.get("fai"):
             shell(
                 "(cd {tmpdir}; {gather} && "
                 "bcftools concat -Oz --naive {names} > concat.vcf.gz && "
                 "bcftools reheader --fai {workdir}/{snakemake.input.fai} concat.vcf.gz "
-                "> {workdir}/{snakemake.output}) {log}"
+                "> {out}) {log}"
             )
         else:
             shell(
                 "(cd {tmpdir}; {gather} && "
                 "bcftools concat -Oz --naive {names} "
-                "> {workdir}/{snakemake.output}) {log}"
+                "> {out}) {log}"
             )
 except subprocess.CalledProcessError as e:
     if snakemake.log: