fix: bug with SE reads (#1395)

<!-- Ensure that the PR title follows conventional commit style (<type>:
<description>)-->
<!-- Possible types are here:
https://github.com/commitizen/conventional-commit-types/blob/master/index.json
-->

### Description

<!-- Add a description of your PR here-->

### QC
<!-- Make sure that you can tick the boxes below. -->

* [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).

bio/bowtie2/align/test/Snakefile

@@ -28,6 +28,22 @@ rule test_bowtie2:
         "master/bio/bowtie2/align"
 
 
+use rule test_bowtie2 as test_bowtie2_se_gz with:
+    input:
+        sample=["reads/{sample}.1.fastq.gz"],
+        idx=multiext(
+            "index/genome",
+            ".1.bt2",
+            ".2.bt2",
+            ".3.bt2",
+            ".4.bt2",
+            ".rev.1.bt2",
+            ".rev.2.bt2",
+        ),
+    output:
+        "mapped_se_gz/{sample}.bam",
+
+
 rule test_bowtie2_index:
     input:
         sample=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],

bio/bowtie2/align/wrapper.py

@@ -41,7 +41,7 @@ def get_format(path: str) -> str:
 
 reads = ""
 if n == 1:
-    if get_format(snakemake.input.sample) in ("bam", "sam"):
+    if get_format(snakemake.input.sample[0]) in ("bam", "sam"):
         reads = f"-b {snakemake.input.sample}"
     else:
         if snakemake.params.get("interleaved", False):

test.py

@@ -1660,6 +1660,11 @@ def test_bowtie2_align():
         ["snakemake", "--cores", "2", "mapped/a.bam", "--use-conda", "-F"],
     )
 
+    run(
+        "bio/bowtie2/align",
+        ["snakemake", "--cores", "2", "mapped_se_gz/a.bam", "--use-conda", "-F"],
+    )
+
 
 @skip_if_not_modified
 def test_bowtie2_build():