fix: account for memory overhead (#2648)

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According to the manual, `-m` specifies the approximated maximum
required memory per thread.
In some cases, `samtools sort` can use more memory than specified (e.g.
samtools/samtools#831) so we account for some
overhead.

### 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,
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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),
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`snakedeploy pin-conda-envs environment.yaml` on a linux machine,
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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),
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usually not needed because most packages are in conda-forge nowadays).

bio/samtools/sort/wrapper.py

@@ -15,7 +15,12 @@
 extra = snakemake.params.get("extra", "")
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
-mem_per_thread_mb = int(get_mem(snakemake) / snakemake.threads)
+# `-m`: Approximately the maximum required memory per thread [...]
+# samtools sort can use more memory than specified (e.g. https://github.com/samtools/samtools/issues/831)
+mem_overhead_factor = snakemake.params.get("mem_overhead_factor", 0.1)
+mem_per_thread_mb = int(
+    get_mem(snakemake) / snakemake.threads * (1.0 - mem_overhead_factor)
+)
 
 with tempfile.TemporaryDirectory() as tmpdir:
     tmp_prefix = Path(tmpdir) / "samtools_sort"