Cooltools insulation

modules/nf-core/cooltools/insulation/environment.yml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::cooltools=0.7.1

modules/nf-core/cooltools/insulation/main.nf

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+process COOLTOOLS_INSULATION {
+    tag "${meta.id}"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/cooltools:0.7.1--py39hff726c5_2' :
+        'biocontainers/cooltools:0.7.1--py39hff726c5_2' }"
+
+    input:
+    tuple val(meta), path(cool)
+
+    output:
+    tuple val(meta), path("*tsv"), emit:tsv
+    tuple val(meta), path("*.bw"), optional: true, emit: bigwig
+    path("versions.yml"), emit:versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    cooltools insulation \\
+        -p ${task.cpus} \\
+        -o ${prefix}_insulation.tsv \\
+        ${cool} \\
+        ${args} \\
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cooltools: \$(cooltools --version 2>&1 | grep version | sed 's/cooltools, version //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_insulation.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cooltools: \$(cooltools --version 2>&1 | grep version | sed 's/cooltools, version //')
+    END_VERSIONS
+    """
+
+}

modules/nf-core/cooltools/insulation/meta.yml

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+name: "cooltools_insulation"
+description: Calculate the diamond insulation scores and call insulating boundaries
+keywords:
+  - cool
+  - insulation
+  - Hi-C
+tools:
+  - "cooltools":
+      description: "Analysis tools for genomic interaction data stored in .cool format"
+      homepage: "https://cooltools.readthedocs.io"
+      documentation: "https://cooltools.readthedocs.io"
+      tool_dev_url: "https://github.com/open2c/cooltools/"
+      doi: "10.5281/zenodo.5214125"
+      licence: ["MIT"]
+      identifier: biotools:cooltools
+
+input:
+  - - meta:
+        type: map
+        description: Groovy Map containing sample information e.g. id:'test'
+    - cool:
+        type: file
+        description: cool file
+        pattern: "*.cool"
+
+output:
+  - tsv:
+      - meta:
+          type: map
+          description: Groovy Map containing sample information e.g. id:'test'
+      - "*tsv":
+          type: file
+          description: tsv file with insulation score and boundaries for several window sizes
+          ontologies:
+          - edam: "http://edamontology.org/format_3475" # TSV
+  - bigwig:
+      - meta:
+          type: map
+          description: Groovy Map containing sample information e.g. id:'test'
+      - "*.bw":
+          type: file
+          description: bigwig file for different window sizes
+          ontologies:
+          - edam: "http://edamontology.org/format_3006" # bigWig
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@nservant"

modules/nf-core/cooltools/insulation/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process COOLTOOLS_INSULATION"
+    script "../main.nf"
+    process "COOLTOOLS_INSULATION"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "cooltools"
+    tag "cooltools/insulation"
+
+    test("homo_sapiens - bam") {
+
+        when {
+            params {
+                modules_testdata_base_path = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/"
+            }
+            process {
+                """
+                input[0] = [ [ id:'test' ],
+                       file(params.modules_testdata_base_path + '/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.balanced.2.cool', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - bam - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                modules_testdata_base_path = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/"
+            }
+            process {
+                """
+                input[0] = [ [ id:'test' ],
+                       file(params.modules_testdata_base_path + '/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.balanced.2.cool', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/cooltools/insulation/tests/main.nf.test.snap

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+{
+    "homo_sapiens - bam": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_insulation.tsv:md5,950b848b7be4bbd63e897bd3989871de"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+                    "versions.yml:md5,49359edc002cbf2d7f08475a768bf565"
+                ],
+                "bigwig": [
+
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_insulation.tsv:md5,950b848b7be4bbd63e897bd3989871de"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,49359edc002cbf2d7f08475a768bf565"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.2"
+        },
+        "timestamp": "2025-06-04T17:09:54.801181735"
+    },
+    "homo_sapiens - bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_insulation.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+                    "versions.yml:md5,49359edc002cbf2d7f08475a768bf565"
+                ],
+                "bigwig": [
+
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_insulation.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,49359edc002cbf2d7f08475a768bf565"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.2"
+        },
+        "timestamp": "2025-06-04T17:10:08.339260848"
+    }
+}