feat: tmpdir in Sambamba wrappers (#960)

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### Description

This PR adds `--tmpdir` parameter in Sambamba sort and markdup.

### 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: tdayris <tdayris@gustaveroussy.fr>
Co-authored-by: tdayris <thibault.dayris@gustaveroussy.fr>
Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Co-authored-by: Felix Mölder <felix.moelder@uni-due.de>
Co-authored-by: Christopher Schröder <christopher.schroeder@tu-dortmund.de>

bio/sambamba/markdup/wrapper.py

@@ -6,11 +6,13 @@
 
 import os
 from snakemake.shell import shell
+from tempfile import TemporaryDirectory
 
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
-shell(
-    "sambamba markdup {snakemake.params.extra} -t {snakemake.threads} "
-    "{snakemake.input[0]} {snakemake.output[0]} "
-    "{log}"
-)
+with TemporaryDirectory() as tempdir:
+    shell(
+        "sambamba markdup {snakemake.params.extra} --nthreads {snakemake.threads} "
+        "--tmpdir {tempdir} {snakemake.input[0]} {snakemake.output[0]} "
+        "{log}"
+    )

bio/sambamba/sort/wrapper.py

@@ -6,11 +6,13 @@
 
 import os
 from snakemake.shell import shell
+from tempfile import TemporaryDirectory
 
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
-shell(
-    "sambamba sort {snakemake.params} -t {snakemake.threads} "
-    "-o {snakemake.output[0]} {snakemake.input[0]} "
-    "{log}"
-)
+with TemporaryDirectory() as tempdir:
+    shell(
+        "sambamba sort {snakemake.params} --nthreads {snakemake.threads} "
+        "--tmpdir {tempdir} --out {snakemake.output[0]} {snakemake.input[0]} "
+        "{log}"
+    )