feat: Rseqc infer experiment (#2730)

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This PR adds [RSeQC
infer_experiment.py](https://rseqc.sourceforge.net/#infer-experiment-py)
to the list of available wrappers.

This is an example of "very simple" wrappers I was talking about in the
PR on `read_gc.py`.

### 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).

---------

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/rseqc/infer_experiment/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - rseqc=5.0.3

bio/rseqc/infer_experiment/meta.yaml

@@ -0,0 +1,13 @@
+name: infer_experiment
+description: Report read strandiness and endeness
+url: https://rseqc.sourceforge.net/#infer-experiment-py
+authors:
+  - "Thibault Dayris"
+input:
+  - aln: Path to SAM/BAM alignment file
+  - refgene: Path to reference gene model in bed format
+output:
+  - Path to text formated results
+params:
+  - extra: Optional parameters for `infer_experiment.py` other than `-i` or `-r`
+

bio/rseqc/infer_experiment/test/Snakefile

@@ -0,0 +1,12 @@
+rule test_rseqc_infer_experiment:
+    input:
+        aln="a.bam",
+        refgene="genes.bed",
+    output:
+        "a.experiment.txt",
+    log:
+        "rseqc/infer_experiment.log",
+    params:
+        extra="-s 4 -q 3",
+    wrapper:
+        "master/bio/rseqc/infer_experiment"

bio/rseqc/infer_experiment/test/genes.bed

@@ -0,0 +1,2 @@
+contig1	6	12	transcript1	0	+	12	12	0	1	6,	0,
+config1	6	16	transcript2	0	+	16	16	0	1	10,	0,

bio/rseqc/infer_experiment/wrapper.py

@@ -0,0 +1,20 @@
+# coding: utf-8
+
+"""Snakemake wrapper for RSeQC infer experiment"""
+
+__author__ = "Thibault Dayris"
+__mail__ = "thibault.dayris@gustaveroussy.fr"
+__copyright__ = "Copyright 2024, Thibault Dayris"
+__license__ = "MIT"
+
+from snakemake import shell
+
+extra = snakemake.params.get("extra", "")
+log = snakemake.log_fmt_shell(stdout=False, stderr=True)
+
+shell(
+    "infer_experiment.py {extra} "
+    "--input-file {snakemake.input.aln} "
+    "--refgene {snakemake.input.refgene} "
+    "> {snakemake.output} {log}"
+)

test.py

@@ -6139,6 +6139,13 @@ def test_generate_data_matrix():
         ["snakemake", "--cores", "1", "--use-conda", "-F"],
     )
 
+@skip_if_not_modified
+def test_rseqc_infer_experiment():
+    run(
+        "bio/rseqc/infer_experiment",
+        ["snakemake", "--cores", "1", "--use-conda", "-F", "a.experiment.txt"],
+    )
+
 
 @skip_if_not_modified
 def test_rseqc_read_gc():