feat: Deeptools multibigwig summary (#3135)

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* [x] `test.py` was updated to call any added or updated example rules
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<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **New Features**
- Introduced new files for setting up Conda environments
(`environment.linux-64.pin.txt`, `environment.yaml`) to streamline
installation for DeepTools.
- Added a `meta.yaml` file providing essential metadata and
configuration for the `deeptools multi bigwig summary` tool.
- Created a `wrapper.py` script to facilitate integration of the
`multiBigwigSummary` command within Snakemake workflows.
- Added test cases for the `multibigwigsummary` command to ensure
functionality with different inputs.

- **Documentation**
- Enhanced user guidance with new configuration files and structured
metadata for better usability in genomic analyses.

- **Tests**
- Included new tests for the `deeptools multibigwigsummary`
functionality to improve coverage and reliability.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

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/multibigwigsummary/environment.linux-64.pin.txt

@@ -0,0 +1,112 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
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bio/deeptools/multibigwigsummary/environment.yaml

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

bio/deeptools/multibigwigsummary/meta.yaml

@@ -0,0 +1,17 @@
+name: deeptools multi bigwig summary
+url: https://deeptools.readthedocs.io/en/develop/content/tools/multiBigwigSummary.html
+description: >
+  Compute the average scores for each of the files in every genomic region.
+authors:
+  - Thibault Dayris
+input:
+  - bw: Path to a bigwig file, or a list of bigwig files.
+  - blacklist: Optional path to a BED file covering regions to exclude.
+  - bed: Path to a bed file to limit the analysis of regions. This triggers the subcommand `BED-file`. Leave empty to run the `bins` subcommand.
+output:
+  - npz: Path to the compressed matrix file.
+  - counts: Path to average scores per region for each bigwig.
+params:
+  - extra: Optional arguments for `multiBigwigSummary` besides IO and processor.
+notes: |
+  Subcomand is automatically inferred from the presence of `input.bed` (optional) key.

bio/deeptools/multibigwigsummary/test/Snakefile

@@ -0,0 +1,33 @@
+rule test_deeptools_multibwsummary_bins:
+    input:
+        bw=["a.bw", "b.bw"],
+        blacklist="blacklist.bed", # Optional
+    output:
+        npz="bins.npz",
+        counts="bins.counts",
+    threads: 1
+    params:
+        extra="",
+    log:
+        "bins.logs"
+    wrapper:
+        "master/bio/deeptools/multibigwigsummary"
+
+rule test_deeptools_multibwsummary_bed:
+    input:
+        bw=["a.bw", "b.bw"],
+        bed="intervals.bed",
+        # blacklist="", # Optional
+    output:
+        npz="bed.npz",
+        counts="bed.counts",
+    threads: 1
+    params:
+        extra="",
+    log:
+        "bins.logs"
+    wrapper:
+        "master/bio/deeptools/multibigwigsummary"
+
+
+

bio/deeptools/multibigwigsummary/test/blacklist.bed

@@ -0,0 +1,2 @@
+1	1	20
+2	15	30

bio/deeptools/multibigwigsummary/test/intervals.bed

@@ -0,0 +1,3 @@
+1	10	40
+1	100	150
+2	1	20

bio/deeptools/multibigwigsummary/wrapper.py

@@ -0,0 +1,36 @@
+# coding: utf-8
+
+__author__ = "Thibault Dayris"
+__copyright__ = "Copyright 2024, Thibault Dayris"
+__email__ = "thibault.dayris@gustaveroussy.fr"
+__license__ = "MIT"
+
+
+from snakemake.shell import shell
+
+# Optional parameters
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+extra = snakemake.params.get("extra", "")
+
+blacklist = snakemake.input.get("blacklist")
+if blacklist:
+    extra += f" --blackListFileName {blacklist} "
+
+out_raw_counts = snakemake.output.get("counts")
+if out_raw_counts:
+    extra += f" --outRawCounts {out_raw_counts} "
+
+bed = snakemake.input.get("bed")
+subcommand = "bins"
+if bed:
+    subcommand = "BED-file"
+    extra += f" --BED {bed} "
+
+
+shell(
+    "multiBigwigSummary {subcommand} "
+    "--bwfiles {snakemake.input.bw} "
+    "--outFileName {snakemake.output.npz} "
+    "--numberOfProcessors {snakemake.threads} "
+    "{extra} {log}"
+)

test.py

@@ -2855,6 +2855,32 @@ def test_deeptools_bamcoverage():
     )
 
 
+@skip_if_not_modified
+def test_deeptools_multibigwigsummary():
+    run(
+        "bio/deeptools/multibigwigsummary",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "--use-conda",
+            "-F",
+            "bins.npz",
+        ],
+    )
+    run(
+        "bio/deeptools/multibigwigsummary",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "--use-conda",
+            "-F",
+            "bed.npz",
+        ],
+    )
+
+
 @skip_if_not_modified
 def test_deeptools_bamcoverage_eff():
     run(