fix: genomepy wrapper (#1795)

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### Description

fixed the genomepy wrapper 🥳 

### 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),
* 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).

---------

Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>

bio/genomepy/meta.yaml

@@ -10,4 +10,3 @@ output: |
   and whether or not it is specified as output.
 params:
   - provider: which provider to download from, defaults to UCSC (choose from UCSC, Ensembl, NCBI).
-blacklisted: fails with ValueError when trying to remove plugin from list

bio/genomepy/test/Snakefile

@@ -6,13 +6,13 @@ rule genomepy:
             ".fa.fai",
             ".fa.sizes",
             ".gaps.bed",
-            ".annotation.gtf.gz",
+            ".annotation.gtf",
             ".blacklist.bed",
         ),
     log:
         "logs/genomepy_{assembly}.log",
     params:
-        provider="UCSC",  # optional, defaults to ucsc. Choose from ucsc, ensembl, and ncbi
+        provider="ucsc",  # optional, defaults to ucsc. Choose from ucsc, ensembl, and ncbi
     cache: "omit-software"  # mark as eligible for between workflow caching
     wrapper:
         "master/bio/genomepy"

bio/genomepy/wrapper.py

@@ -7,7 +7,7 @@
 from snakemake.shell import shell
 
 # Optional parameters
-provider = snakemake.params.get("provider", "UCSC")
+provider = snakemake.params.get("provider", "ucsc").lower()
 
 # set options for plugins
 all_plugins = "blacklist,bowtie2,bwa,gmap,hisat2,minimap2,star"
@@ -40,6 +40,6 @@
 
     # install the genome
     genomepy install {snakemake.wildcards.assembly} \
-    {provider} {annotation} -g {genome_dir} >> {log} 2>&1
+    --provider {provider} {annotation} -g {genome_dir} >> {log} 2>&1
     """
 )