feat: Deeptools bampefragmentsize

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

@@ -0,0 +1,123 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
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+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_2.conda#048b02e3962f066da18efe3a21b77672
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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 +1,52 @@
+__author__ = "Niek Wit"
+__copyright__ = "Copyright 2025, Niek Wit"
+__email__ = "niekwit@gmail.com"
+__license__ = "MIT"
+
+import os
+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 = [os.path.basename(bam.replace(".bam", "")) for bam in bam_files]
+
+# 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.get("hist")).suffix
+VALID_FORMATS = {".png", ".pdf", ".svg", ".eps", ".plotly"}
+if not out_format 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}"
+)