feat: Support lists in param.region, and fix typo (#2978)

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### 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).

bio/samtools/faidx/test/Snakefile

@@ -38,16 +38,31 @@ rule samtools_faidx_bgzip:
         "master/bio/samtools/faidx"
 
 
-rule samtools_faidx_region:
+rule samtools_faidx_region_file:
     input:
         "{sample}.fa",
         fai="idx/{sample}.fa.fai",
+        regions="{sample}.regions",
     output:
-        "out/{sample}.fas",
+        "out/{sample}.region_file.fas",
     log:
-        "{sample}.region.log",
+        "{sample}.region_file.log",
     params:
-        region="ref",
+        extra="--length 5",
+    wrapper:
+        "master/bio/samtools/faidx"
+
+
+rule samtools_faidx_region_array:
+    input:
+        "{sample}.fa",
+        fai="idx/{sample}.fa.fai",
+    output:
+        "out/{sample}.region_array.fas",
+    log:
+        "{sample}.region_array.log",
+    params:
+        region=["ref", "ref2"],
         extra="--length 5",
     wrapper:
         "master/bio/samtools/faidx"
@@ -59,9 +74,9 @@ rule samtools_faidx_bgzip_region:
         fai="idx/{sample}.fa.bgz.fai",
         gzi="idx/{sample}.fa.bgz.gzi",
     output:
-        "out/{sample}.bgz.fas",
+        "out/{sample}.region_bgzip.fas",
     log:
-        "{sample}.bgzip_region.log",
+        "{sample}.region_bgzip.log",
     params:
         region="ref",
         extra="--length 5",

bio/samtools/faidx/test/genome.regions

@@ -0,0 +1 @@
+ref

bio/samtools/faidx/wrapper.py

@@ -17,10 +17,11 @@
 # Get regions (if present)
 regions = snakemake.input.get("regions", "")
 if regions:
-    regions = f"--regions-file {regions}"
+    regions = f"--region-file {regions}"
 
 region = snakemake.params.get("region", "")
 
+
 # Get FAI and GZI files
 if region or regions:
     fai = snakemake.input.get("fai", "")

test.py

@@ -4242,8 +4242,9 @@ def test_samtools_faidx():
             "out/genome.named.fa.fai",
             "out/genome.fas.bgz.fai",
             "out/genome.fas.bgz.gzi",
-            "out/genome.fas",
-            "out/genome.bgz.fas",
+            "out/genome.region_file.fas",
+            "out/genome.region_array.fas",
+            "out/genome.region_bgzip.fas",
             "--use-conda",
             "-F",
         ],