feat: auto infer run mode (#2937)

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### QC
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Auto infers if it should compress or decompress.

* [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).

---------

Co-authored-by: Christian Meesters <cmeesters@users.noreply.github.com>

bio/bgzip/meta.yaml

@@ -3,7 +3,12 @@ description: Block compression/decompression utility
 url: https://github.com/samtools/htslib
 authors:
   - William Rowell
+  - Filipe G. Vieira
 input:
   - file to be compressed or decompressed
 output:
-  - compressed or decompressed output
+  - compressed or decompressed output
+params:
+  - extra: additional bgzip parameters
+notes: |
+  * Run mode (compression/decompression) is automatically inferred from the extension of the input file.

bio/bgzip/wrapper.py

@@ -9,9 +9,11 @@
 extra = snakemake.params.get("extra", "")
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
+
+if snakemake.input[0].endswith(".gz"):
+    extra += " --decompress"
+
+
 shell(
-    """
-    (bgzip -c {extra} --threads {snakemake.threads} \
-        {snakemake.input} > {snakemake.output}) {log}
-    """
+    "bgzip --threads {snakemake.threads} {extra} --output {snakemake.output[0]} {snakemake.input[0]} {log}"
 )