test: add test for creating bai index using bwa mem (snakemake#2927)

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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).

Author: Smeds

bio/bwa/mem/test/Snakefile_samtools

@@ -17,13 +17,32 @@ rule bwa_mem:
         "master/bio/bwa/mem"
 
 
-rule bwa_mem_write_index:
+rule bwa_mem_write_index_csi:
     input:
         reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
         idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
     output:
-        "mapped_with_index/{sample}.bam",
-        idx="mapped_with_index/{sample}.bam.csi",
+        "mapped_with_index_csi/{sample}.bam",
+        idx="mapped_with_index_csi/{sample}.bam.csi",
+    log:
+        "logs/bwa_mem/{sample}.log",
+    params:
+        extra=r"-R '@RG\tID:{sample}\tSM:{sample}'",
+        sorting="samtools",  # Can be 'none', 'samtools' or 'picard'.
+        sort_order="coordinate",  # Can be 'queryname' or 'coordinate'.
+        sort_extra="",  # Extra args for samtools/picard.
+        tmp_dir="/tmp/",  # Path to temp dir. (optional)
+    threads: 8
+    wrapper:
+        "master/bio/bwa/mem"
+
+rule bwa_mem_write_index_bai:
+    input:
+        reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
+        idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
+    output:
+        "mapped_with_index_bai/{sample}.bam",
+        idx="mapped_with_index_bai/{sample}.bam.bai",
     log:
         "logs/bwa_mem/{sample}.log",
     params:

test.py

@@ -2141,8 +2141,22 @@ def test_bwa_mem_sort_samtools_write_index():
             "snakemake",
             "--cores",
             "1",
-            "mapped_with_index/a.bam",
-            "mapped_with_index/a.bam.csi",
+            "mapped_with_index_csi/a.bam",
+            "mapped_with_index_csi/a.bam.csi",
+            "--use-conda",
+            "-F",
+            "-s",
+            "Snakefile_samtools",
+        ],
+    )
+    run(
+        "bio/bwa/mem",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "mapped_with_index_bai/a.bam",
+            "mapped_with_index_bai/a.bam.bai",
             "--use-conda",
             "-F",
             "-s",