fix: Add tests to Sickle and fixed typo (#1126)

<!-- 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-->

Fixing issue #1125 

### 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/sickle/pe/test/Snakefile

@@ -1,17 +1,16 @@
 rule sickle_pe:
   input:
-    r1="input_R1.fq",
-    r2="input_R2.fq"
+    r1="reads/{sample}.1.fastq",
+    r2="reads/{sample}.2.fastq"
   output:
-    r1="output_R1.fq",
-    r2="output_R2.fq",
-    rs="output_single.fq",
+    r1="{sample}.1.fastq",
+    r2="{sample}.2.fastq",
+    rs="{sample}.single.fastq",
+  log:
+    "logs/sickle/{sample}.log"
   params:
     qual_type="sanger",
     # optional extra parameters
     extra=""
-  log:
-    # optional log file
-    "logs/sickle/job.log"
   wrapper:
     "master/bio/sickle/pe"

bio/sickle/pe/test/reads/a.1.fastq

@@ -0,0 +1,4 @@
+@1
+ACGGCAT
++
+!!!!!!!

bio/sickle/pe/test/reads/a.2.fastq

@@ -0,0 +1,4 @@
+@1
+ACGGCAT
++
+!!!!!!!

bio/sickle/se/test/Snakefile

@@ -1,13 +1,13 @@
-rule sickle_pe:
+rule sickle_se:
   input:
-    "input_R1.fq"
+    "reads/{sample}.1.fastq"
   output:
-    "output_R1.fq"
+    "{sample}.1.fastq"
+  log:
+    "logs/sickle/{sample}.log"
   params:
     qual_type="sanger",
     # optional extra parameters
     extra=""
-  log:
-    "logs/sickle/job.log"
   wrapper:
-    "master/bio/sickle/pe"
+    "master/bio/sickle/se"

bio/sickle/se/test/reads/a.1.fastq

@@ -0,0 +1,4 @@
+@1
+ACGGCAT
++
+!!!!!!!

test.py

@@ -139,6 +139,35 @@ def run(wrapper, cmd, check_log=None):
             os.chdir(origdir)
 
 
+
+@skip_if_not_modified
+def test_sickle_pe():
+    run(
+        "bio/sickle/pe",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "--use-conda",
+            "a.1.fastq",
+            "a.2.fastq",
+            "a.single.fastq",
+        ],
+    )
+
+@skip_if_not_modified
+def test_sickle_se():
+    run(
+        "bio/sickle/se",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "--use-conda",
+            "a.1.fastq",
+        ],
+    )
+
 @skip_if_not_modified
 def test_bwa_memx_index():
     run(