Add new component: deeptools/bamcompare

modules/nf-core/deeptools/bamcompare/environment.yml

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+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::deeptools=3.5.6

modules/nf-core/deeptools/bamcompare/main.nf

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+// This module was written employing Seqera AI (https://seqera.io/ask-ai/chat-v2)
+process DEEPTOOLS_BAMCOMPARE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/deeptools:3.5.6--pyhdfd78af_0' :
+        'quay.io/biocontainers/deeptools:3.5.6--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(bam1), path(bai1), path(bam2), path(bai2)
+
+    output:
+    tuple val(meta), path("*.bigWig")  , emit: bigwig  , optional: true
+    tuple val(meta), path("*.bedgraph"), emit: bedgraph, optional: true
+    tuple val("${task.process}"), val('deeptools'), eval('bamCompare --version | sed "s/bamCompare //g"') , emit: versions_deeptools, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    // Determine output format from args or default to bigwig
+    def format = args.contains('--outFileFormat bedgraph') ? 'bedgraph' : 'bigWig'
+    def output_file = "${prefix}.${format}"
+
+    """
+    bamCompare \\
+        --bamfile1 $bam1 \\
+        --bamfile2 $bam2 \\
+        --outFileName $output_file \\
+        --numberOfProcessors $task.cpus \\
+        $args
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def format = args.contains('--outFileFormat bedgraph') ? 'bedgraph' : 'bigWig'
+    def output_file = "${prefix}.${format}"
+
+    """
+    touch $output_file
+    """
+}

modules/nf-core/deeptools/bamcompare/meta.yml

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+name: "deeptools_bamcompare"
+description: Compares two BAM files based on the number of mapped reads and
+  generates a bigWig or bedGraph file with the log2 ratio, ratio, difference or
+  other operations.
+keywords:
+  - bam
+  - bigwig
+  - bedgraph
+  - normalization
+  - comparison
+tools:
+  - deeptools:
+      description: A set of user-friendly tools for normalization and
+        visualization of deep-sequencing data
+      homepage: https://deeptools.readthedocs.io/en/latest/
+      documentation: https://deeptools.readthedocs.io/en/latest/content/tools/bamCompare.html
+      tool_dev_url: https://github.com/deeptools/deepTools
+      doi: "10.1093/nar/gkw257"
+      licence:
+        - "GPL v3"
+      identifier: biotools:deeptools
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
+    - bam1:
+        type: file
+        description: Sorted BAM file 1 (usually treatment)
+        pattern: "*.{bam}"
+        ontologies:
+          - edam: "http://edamontology.org/format_2572" # BAM
+    - bai1:
+        type: file
+        description: BAM index file for BAM file 1
+        pattern: "*.{bai}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3327" # BAI
+    - bam2:
+        type: file
+        description: Sorted BAM file 2 (usually control)
+        pattern: "*.{bam}"
+        ontologies:
+          - edam: "http://edamontology.org/format_2572" # BAM
+    - bai2:
+        type: file
+        description: BAM index file for BAM file 2
+        pattern: "*.{bai}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3327" # BAI
+output:
+  bigwig:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*.bigWig":
+          type: file
+          description: BigWig coverage file of comparison results
+          pattern: "*.{bigWig}"
+          ontologies:
+            - edam: "http://edamontology.org/format_3006" # bigWig
+  bedgraph:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*.bedgraph":
+          type: file
+          description: BedGraph coverage file of comparison results
+          pattern: "*.{bedgraph}"
+          ontologies:
+            - edam: "http://edamontology.org/format_3583" # BedGraph
+  versions_deeptools:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - deeptools:
+          type: string
+          description: The name of the tool
+      - bamCompare --version | sed "s/bamCompare //g":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - deeptools:
+          type: string
+          description: The name of the tool
+      - bamCompare --version | sed "s/bamCompare //g":
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@seqeraai"
+  - "@oliverdrechsel"
+maintainers:
+  - "@oliverdrechsel"

modules/nf-core/deeptools/bamcompare/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process DEEPTOOLS_BAMCOMPARE"
+    script "../main.nf"
+    process "DEEPTOOLS_BAMCOMPARE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "deeptools"
+    tag "deeptools/bamcompare"
+
+    config "./nextflow.config"
+
+    test("sarscov2 - bam - bigwig") {
+
+        when {
+            params {
+                module_args = ''
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - bedgraph") {
+
+        when {
+            params {
+                module_args = '--outFileFormat bedgraph --binSize 10'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.bedgraph,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                module_args = ''
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/deeptools/bamcompare/tests/main.nf.test.snap

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+{
+    "sarscov2 - bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bigWig:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+                    [
+                        "DEEPTOOLS_BAMCOMPARE",
+                        "deeptools",
+                        "3.5.6"
+                    ]
+                ],
+                "bedgraph": [
+
+                ],
+                "bigwig": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bigWig:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_deeptools": [
+                    [
+                        "DEEPTOOLS_BAMCOMPARE",
+                        "deeptools",
+                        "3.5.6"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-07T12:55:58.917296921",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "sarscov2 - bam - bedgraph": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.bedgraph:md5,63141eeba79301006699cdee4abf0ff1"
+                ]
+            ],
+            null
+        ],
+        "timestamp": "2026-05-07T12:55:08.239773859",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "sarscov2 - bam - bigwig": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bigWig:md5,c59753155328f9b0dc56746cca440d90"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+                    [
+                        "DEEPTOOLS_BAMCOMPARE",
+                        "deeptools",
+                        "3.5.6"
+                    ]
+                ],
+                "bedgraph": [
+
+                ],
+                "bigwig": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bigWig:md5,c59753155328f9b0dc56746cca440d90"
+                    ]
+                ],
+                "versions_deeptools": [
+                    [
+                        "DEEPTOOLS_BAMCOMPARE",
+                        "deeptools",
+                        "3.5.6"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-07T12:54:16.387360777",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    }
+}

modules/nf-core/deeptools/bamcompare/tests/nextflow.config

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+process {
+    withName: 'DEEPTOOLS_BAMCOMPARE' {
+        ext.args = params.module_args ?: ''
+    }
+}

modules/nf-core/deeptools/bamcompare/tests/tags.yml

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+deeptools/bamcompare:
+  - "modules/nf-core/deeptools/bamcompare/**"
+  - "tests/modules/nf-core/deeptools/bamcompare/**"