feat: Deeptools bampefragmentsize (#3596)

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### QC
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* [x] I confirm that I have followed the [documentation for contributing
to
`snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html).

While the contributions guidelines are more extensive, please
particularly ensure that:
* [x] `test.py` was updated to call any added or updated example rules
in a `Snakefile`
* [x] `input:` and `output:` file paths in the rules can be chosen
arbitrarily
* [x] wherever possible, command line arguments are inferred and set
automatically (e.g. based on file extensions in `input:` or `output:`)
* [ ] 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
* [x] the `meta.yaml` contains a link to the documentation of the
respective tool or command under `url:`
* [x] conda environments use a minimal amount of channels and packages,
in recommended ordering

This is my first Snakemake wrapper. I hope to contribute more later.


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
- Added support for calculating fragment sizes from paired-end BAM files
using DeepTools.
- Introduced a new workflow tool for generating fragment size histograms
and raw length data.
- Created a new Conda environment configuration for setting up the
DeepTools package.
	- Added a new file specifying regions for analysis.

- **Documentation**
- Created comprehensive metadata for the DeepTools fragment size
analysis tool, including usage instructions and output specifications.

- **Tests**
- Added test case for the new DeepTools fragment size analysis
functionality.
- Enhanced test coverage with multiple scenarios for the fragment size
analysis tool.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: Filipe G. Vieira <[email protected]>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

bio/deeptools/bampefragmentsize/environment.linux-64.pin.txt

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+# $ conda create --name <env> --file <this file>
+# platform: linux-64
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+https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-qthelp-2.0.0-pyhd8ed1ab_1.conda#00534ebcc0375929b45c3039b5ba7636
+https://conda.anaconda.org/conda-forge/noarch/sphinx-8.1.3-pyhd8ed1ab_1.conda#1a3281a0dc355c02b5506d87db2d78ac
+https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-serializinghtml-1.1.10-pyhd8ed1ab_1.conda#3bc61f7161d28137797e038263c04c54

bio/deeptools/bampefragmentsize/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - deeptools =3.5.5

bio/deeptools/bampefragmentsize/meta.yaml

@@ -0,0 +1,34 @@
+name: deepTools bamPEFragmentSize
+url: https://deeptools.readthedocs.io/en/latest/content/tools/bamPEFragmentSize.html
+description: >
+  bamPEFragmentSize calculates the fragment sizes for read pairs in paired-end sequencing BAM files.
+  It generates a histogram of fragment sizes and can output the raw fragment length data.
+  For usage information about ``deepTools bamPEFragmentSize``, please see the [documentation](https://deeptools.readthedocs.io/en/latest/content/tools/bamPEFragmentSize.html).
+  For more information about ``deepTools``, also see the [source code](https://github.com/deeptools/deepTools).
+
+options:
+  histogram:
+    flags: ["--histogram", "-hist", "-o"]
+    format: "image file"
+    variable: "hist"
+    extension: ".png"
+    required: true
+  raw_lengths:
+    flag: "--outRawFragmentLengths"
+    format: "tab-separated table of fragment lengths and occurrences"
+    variable: "raw"
+    extension: ".tab"
+    required: false
+
+authors:
+  - Niek Wit
+input:
+  - bams: List of BAM files (.bam)
+  - blacklist: Optional BED file with regions to skip (.bed)
+output:
+  - hist: Fragment size histogram (.png)
+  - raw: Raw fragment lengths (.tab) (optional)
+params:
+  - label: Labels for plotting (list of string or "" for automatic labelling)
+  - extra: Optional parameters given to bamPEFragmentSize
+

bio/deeptools/bampefragmentsize/test/Snakefile

@@ -0,0 +1,29 @@
+rule deeptools_bampe_fragmentsize:
+    input:
+        # Input BAM file(s)
+        bams=["a.bam", "b.bam"],
+        # Optional blacklist file in BED format to exclude specific regions from analysis
+        # blacklist="",
+    output:
+        # Please note that -o/hist/--histogram and --outRawFragmentLengths are exclusively defined via output files.
+        # Usable output variables, their extensions and which option they implicitly call are listed here:
+        # https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/deeptools/bamPEFragmentSize.html.
+        # Required
+        hist="results/histogram.png",
+        # Optional output files
+        raw="results/raw.tab",
+    log:
+        "logs/deeptools/bampe_fragmentsize.log",
+    threads: 4
+    params:
+        # Labels can be changed to anything
+        # If left empty, the sample name will be used 
+        # (without path and .bam extension)
+        # Format: list matching the number of input BAMs
+        # Example: ["sample1", "sample2"] or "" for automatic labels
+        labels="",
+        # Additional parameters for deeptools bamPEFragmentSize
+        # Example: --maxFragmentLength 1000 --binSize 10
+        extra="--logScale",
+    wrapper:
+        "master/bio/deeptools/bampefragmentsize"

bio/deeptools/bampefragmentsize/test/regions.bed

@@ -0,0 +1,2 @@
+1   10000 20000
+1   20000   40000

bio/deeptools/bampefragmentsize/wrapper.py

@@ -0,0 +1,51 @@
+__author__ = "Niek Wit"
+__copyright__ = "Copyright 2025, Niek Wit"
+__email__ = "[email protected]"
+__license__ = "MIT"
+
+from pathlib import Path
+from snakemake.shell import shell
+
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
+# Get input files
+# Let Snakemake handle the error if bams are missing
+bam_files = snakemake.input.bams
+blacklist = snakemake.input.get("blacklist", "")
+if blacklist:
+    blacklist = f"--blackListFileName {blacklist}"
+
+# Get/create sample labels (remove .bam extension and dir)
+# If no labels are provided, use the basename of the bam file
+sample_label = snakemake.params.get("labels", "")
+if not sample_label:
+    sample_label = [Path(bam).stem for bam in bam_files if Path(bam).suffix == ".bam"]
+
+# Check if the number of labels is equal to the number of bam files
+assert len(sample_label) == len(
+    bam_files
+), "Number of labels must be equal to the number of bam files"
+
+# Check output format
+out_format = Path(snakemake.output.hist).suffix
+VALID_FORMATS = {".png", ".pdf", ".svg", ".eps", ".plotly"}
+if out_format not in VALID_FORMATS:
+    raise ValueError(
+        f"Invalid output format '{out_format}'. Must be one of: {', '.join(sorted(VALID_FORMATS))}"
+    )
+
+# Optional output
+out_raw = snakemake.output.get("raw", "")
+if out_raw:
+    out_raw = f"--outRawFragmentLengths {out_raw}"
+
+# Parameters
+extra = snakemake.params.get("extra", "")
+
+shell(
+    "bamPEFragmentSize "
+    "--numberOfProcessors {snakemake.threads} "
+    "-b {bam_files} "
+    "-o {snakemake.output.hist} "
+    "{blacklist} {out_raw} {extra} {log}"
+)