feat: gatk collectreadcount wrapper (#1315)

### Description

Add a wrapper for gatk collect read count 

### QC

* [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).

---------

Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>

bio/gatk/collectreadcounts/environment.yaml

@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - gatk4 =4.4.0.0
+  - snakemake-wrapper-utils =0.5.3

bio/gatk/collectreadcounts/meta.yaml

@@ -0,0 +1,15 @@
+name: gatk CollectReadCounts
+url: https://gatk.broadinstitute.org/hc/en-us/articles/360037592671-CollectReadCounts
+description: |
+  Collects read counts at specified intervals. The count for each interval is calculated by counting the number of read starts that lie in the interval. 
+authors:
+  - Patrik Smeds
+input:
+  - bam: BAM/SAM/CRAM file containing reads
+  - intervals: one or more genomic intervals over which to operate
+params:
+  - mergingRule: interval merging rule for abutting intervals (default, OVERLAPPING_ONLY)
+  - java_opts: additional arguments to be passed to the java compiler, e.g. "-XX:ParallelGCThreads=10" (not for `-XmX` or `-Djava.io.tmpdir`, since they are handled automatically).
+  - extra: additional program arguments.
+output:
+  - counts: output file for read counts, `tsv` or `hdf5`

bio/gatk/collectreadcounts/test/Snakefile

@@ -0,0 +1,15 @@
+rule collectreadcounts:
+    input:
+        bam=["mapped/a.bam"],
+        intervals=["a.interval_list"],
+    output:
+        counts="a.counts.hdf5",
+    log:
+        "logs/gatk/collectreadcounts.log",
+    params:
+        extra="",  # optional
+        java_opts="",  # optional
+    resources:
+        mem_mb=1024,
+    wrapper:
+        "master/bio/gatk/collectreadcounts"

bio/gatk/collectreadcounts/test/a.interval_list

@@ -0,0 +1,4 @@
+@HD     VN:1.6  SO:coordinate
+@SQ	SN:ref	LN:45
+@SQ	SN:ref2	LN:40
+ref2	1	30	+	TEST

bio/gatk/collectreadcounts/wrapper.py

@@ -0,0 +1,29 @@
+__author__ = "Patrik Smeds"
+__copyright__ = "Copyright 2023, Patrik Smed"
+__email__ = "patrik.smeds@gmail.com"
+__license__ = "MIT"
+
+
+import tempfile
+from snakemake.shell import shell
+from snakemake_wrapper_utils.java import get_java_opts
+
+
+extra = snakemake.params.get("extra", "")
+java_opts = get_java_opts(snakemake)
+
+mergingRule = snakemake.params.get("mergingRule", "OVERLAPPING_ONLY")
+
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
+with tempfile.TemporaryDirectory() as tmpdir:
+    shell(
+        "gatk --java-options '{java_opts}' CollectReadCounts"
+        " -I {snakemake.input.bam}"
+        " -L {snakemake.input.intervals}"
+        " --interval-merging-rule {mergingRule}"
+        " {extra}"
+        " --tmp-dir {tmpdir}"
+        " --output {snakemake.output.counts}"
+        " {log}"
+    )

test.py

@@ -3966,6 +3966,12 @@ def test_gatk_baserecalibratorspark():
         ["snakemake", "--cores", "1", "recal/a.grp", "--use-conda", "-F"],
     )
 
+@skip_if_not_modified
+def test_gatk_collectreadcounts():
+    run(
+        "bio/gatk/collectreadcounts",
+        ["snakemake", "--cores", "1", "a.counts.hdf5", "--use-conda", "-F"],
+    )
 
 @skip_if_not_modified
 def test_gatk_collectalleliccounts():