feat: deeptools bamcoverage (#1237)

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### Description

Provide new wrapper for [DeepTools
bamcoverage](https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html).

### 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),
* 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: tdayris <tdayris@gustaveroussy.fr>
Co-authored-by: tdayris <thibault.dayris@gustaveroussy.fr>
Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Co-authored-by: Felix Mölder <felix.moelder@uni-due.de>
Co-authored-by: Christopher Schröder <christopher.schroeder@tu-dortmund.de>

bio/deeptools/bamcoverage/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - deeptools =3.5.1

bio/deeptools/bamcoverage/meta.yaml

@@ -0,0 +1,17 @@
+name: deepTools bamcoverage
+url: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html?highlight=bamcoverage
+description: >
+  ``deepTools bamcoverage`` takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output. 
+  For more information about ``deepTools``, also see the `source code <https://github.com/deeptools/deepTools>`_.
+authors:
+  - Thibault Dayris
+input:
+  - bam: Path to alignment (BAM) file
+  - blacklist: Path to optional blacklist region file (BED)
+output:
+  - Path to coverage file
+params:
+  - effective_genome_size: Optional effective genome size value
+  - genome: Optional parameter used to fill effective genome size with pre-computed parameters. Can only be one of `GRCm37`, `GRCm38`, `GRCh37`, `GRCh38`, `dm3`, `dm6`, `WBcel235`, or `GRCz10`.
+  - read_length: Optional parameter used to fill effective genome size with pre-computed parameters. Can only be one of `50`, `75`, `100`, `150`, or `200`.
+  - extra: Optional parameters to be given to deepTools bamcoverage

bio/deeptools/bamcoverage/test/Snakefile

@@ -0,0 +1,15 @@
+rule test_deeptools_bamcoverage:
+    input:
+        bam="a.sorted.bam",
+        bai="a.sorted.bam.bai",
+        # Optional path to a blacklist bed file
+        # blacklist="",
+    output:
+        "a.coverage.bw",
+    params:
+        effective_genome_size=1000,
+        extra="",
+    log:
+        "logs/coverage.log",
+    wrapper:
+        "master/bio/deeptools/bamcoverage"

bio/deeptools/bamcoverage/wrapper.py

@@ -0,0 +1,107 @@
+__author__ = "Thibault Dayris"
+__copyright__ = "Copyright 2022, Thibault Dayris"
+__email__ = "thibault.dayris@gustaveroussy.fr"
+__license__ = "MIT"
+
+from snakemake.shell import shell
+
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+extra = snakemake.params.get("extra", "")
+
+# See: https://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html
+default_effective_genome_size = {
+    "GRCz10": {
+        "50": 1195445591,
+        "75": 1251132686,
+        "100": 1280189044,
+        "150": 1312207169,
+        "200": 1321355241,
+    },
+    "WBcel235": {
+        "50": 95159452,
+        "75": 96945445,
+        "100": 98259998,
+        "150": 98721253,
+        "200": 98672758,
+    },
+    "dm3": {
+        "50": 130428560,
+        "75": 135004462,
+        "100": 139647232,
+        "150": 144307808,
+        "200": 148524010,
+    },
+    "dm6": {
+        "50": 125464728,
+        "75": 127324632,
+        "100": 129789873,
+        "150": 129941135,
+        "200": 132509163,
+    },
+    "GRCh37": {
+        "50": 2685511504,
+        "75": 2736124973,
+        "100": 2776919808,
+        "150": 2827437033,
+        "200": 2855464000,
+    },
+    "GRCh38": {
+        "50": 2701495761,
+        "75": 2747877777,
+        "100": 2805636331,
+        "150": 2862010578,
+        "200": 2887553303,
+    },
+    "GRCm37": {
+        "50": 2304947926,
+        "75": 2404646224,
+        "100": 2462481010,
+        "150": 2489384235,
+        "200": 2513019276,
+    },
+    "GRCm38": {
+        "50": 2308125349,
+        "75": 2407883318,
+        "100": 2467481108,
+        "150": 2494787188,
+        "200": 2520869189,
+    },
+}
+
+effective_genome_size = snakemake.params.get("effective_genome_size")
+if not effective_genome_size:
+    genome = snakemake.params.get("genome")
+    read_length = snakemake.params.get("read_length")
+    if genome and read_length:
+        effective_genome_size = "--effectiveGenomeSize "
+        effective_genome_size += default_effective_genome_size[genome][str(read_length)]
+else:
+    effective_genome_size = "--effectiveGenomeSize " + str(effective_genome_size)
+
+
+output_format = ""
+bigwig_format = ["bw", "bigwig"]
+bedgraph_format = ["bg", "bedgraph"]
+output_ext = str(snakemake.output[0]).split(".")[-1].lower()
+if output_ext in bigwig_format:
+    output_format = "bigwig"
+elif output_ext in bedgraph_format:
+    output_format = "bedgraph"
+else:
+    raise ValueError("Output file should be either a bigwig or a bedgraph file")
+
+
+blacklist = snakemake.input.get("blacklist", "")
+if blacklist:
+    blacklist = "--blackListFileName " + blacklist
+
+shell(
+    "bamCoverage "
+    "{blacklist} {extra} "
+    "--numberOfProcessors {snakemake.threads} "
+    "{effective_genome_size} "
+    "--bam {snakemake.input.bam} "
+    "--outFileName {snakemake.output} "
+    "--outFileFormat {output_format} "
+    "{log} "
+)

test.py

@@ -2310,6 +2310,20 @@ def test_deeptools_computematrix():
 
 
 @skip_if_not_modified
+def test_deeptools_bamcoverage():
+    run(
+        "bio/deeptools/bamcoverage",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "a.coverage.bw",
+            "--use-conda",
+            "-F",
+        ],
+    )
+
+@skip_if_not_modified   
 def test_deeptools_alignmentsieve():
     run(
         "bio/deeptools/alignmentsieve",
@@ -2323,7 +2337,6 @@ def test_deeptools_alignmentsieve():
         ],
     )
 
-
 @skip_if_not_modified
 def test_deeptools_plotheatmap():
     run(