feat: deeptools plotcoverage (#1241)

<!-- 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 Deeptools plotcoverage to the list of available wrappers

### 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).

---------

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

bio/deeptools/plotcoverage/environment.yaml

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

bio/deeptools/plotcoverage/meta.yaml

@@ -0,0 +1,15 @@
+name: deepTools plotCoverage
+url: https://deeptools.readthedocs.io/en/develop/content/tools/plotCoverage.html
+description: >
+  ``deepTools plotCoverage`` assess the sequencing depth of given samples.
+  For more information about ``deepTools``, also see the `source code <https://github.com/deeptools/deepTools>`_.
+authors:
+  - Thibault Dayris
+input:
+  - bams: Path to alignment (BAM)
+  - bed: Path to region file (BED)
+  - blacklist: Path to blacklisted regions (BED)
+output:
+  - raw_counts: Raw coverage plot
+  - metrics: Raw coverage metrics
+  - plot: Path to image

bio/deeptools/plotcoverage/test/Snakefile

@@ -0,0 +1,20 @@
+rule test_deeptools_plotcoverage:
+    input:
+        # Optional blacklisted regions
+        # blacklist="",
+        # Optional region file
+        # bed="",
+        bams=["a.bam"],
+        bais=["a.bam.bai"],
+    output:
+        plot="coverage.png",
+        # Optional raw counts
+        raw_counts="coverage.raw",
+        # Optional metrics
+        metrics="coverage.metrics",
+    params:
+        extra="--coverageThresholds 1",
+    log:
+        "logs/deeptools/coverage.log"
+    wrapper:
+        "master/bio/deeptools/plotcoverage"

bio/deeptools/plotcoverage/wrapper.py

@@ -0,0 +1,57 @@
+__author__ = "Thibault Dayris"
+__copyright__ = "Copyright 2023, 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", "")
+
+
+bed = snakemake.input.get("bed", "")
+if bed:
+    bed = " --BED " + bed
+
+
+raw_counts = snakemake.output.get("raw_counts", "")
+if raw_counts:
+    raw_counts = " --outRawCounts " + raw_counts
+
+
+metrics = snakemake.output.get("metrics", "")
+if metrics:
+    metrics = " --outCoverageMetrics " + metrics
+    if not "--coverageThresholds" in extra:
+        raise ValueError(
+            "Coverage metrics without a `--coverageThresholds` in "
+            "extra parameters will result in an empty file. Please "
+            "provide `--coverageThresholds` or remove "
+            "metrics file from expected output files."
+        )
+
+
+blacklist = snakemake.input.get("blacklist", "")
+if blacklist:
+    blacklist = " --blackListFileName " + blacklist
+
+
+accepted_extensions = ["eps", "png", "svg", "pdf"]
+out_image_extension = str(snakemake.output["plot"]).split(".")[-1]
+if out_image_extension not in accepted_extensions:
+    raise ValueError(
+        "Wrong image format: {ext}, expected: {expected}".format(
+            ext=out_image_extension, expected=str(accepted_extensions)
+        )
+    )
+
+
+shell(
+    "plotCoverage "
+    "{extra} {bed} {raw_counts} {metrics} {blacklist} "
+    "--numberOfProcessors {snakemake.threads} "
+    "--bamfiles {snakemake.input.bams} "
+    "--plotFile {snakemake.output.plot} "
+    "--plotFileFormat {out_image_extension} "
+    " {log}"
+)

test.py

@@ -2388,6 +2388,21 @@ def test_deeptools_plotprofile():
     )
 
 
+@skip_if_not_modified
+def test_deeptools_plotcoverage():
+    run(
+        "bio/deeptools/plotcoverage",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "coverage.png",
+            "--use-conda",
+            "-F",
+        ],
+    )
+
+
 @skip_if_not_modified
 def test_deepvariant():
     run(