New module: regtools junction extract

modules/nf-core/regtools/junctionsextract/environment.yml

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+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::regtools=0.5.0"

modules/nf-core/regtools/junctionsextract/main.nf

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+process REGTOOLS_JUNCTIONSEXTRACT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "bioconda::regtools=0.5.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b6/b6c0653189b95b22e16038f61ade205a865857f54eeae9ba0184490a1834f7c9/data' :
+        'community.wave.seqera.io/library/regtools:0.5.0--b9a260c4c898354a' }"
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+
+    output:
+    tuple val(meta), path("*.junc"), emit: junc
+    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}"
+    """
+    regtools junctions extract \\
+        $args \\
+        -o ${prefix}.junc \\
+        $bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        regtools: \$(regtools --version 2>&1 | grep "Version:" | sed 's/Version:\t//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.junc
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        regtools: \$(regtools --version 2>&1 | grep "Version:" | sed 's/Version:\t//')
+    END_VERSIONS
+    """
+}

modules/nf-core/regtools/junctionsextract/meta.yml

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+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "regtools_junctionsextract"
+description: Extract exon-exon junctions from an RNAseq BAM file. The output is a
+  BED file in the BED12 format.
+keywords:
+  - regtools
+  - leafcutter
+  - RNA-seq
+  - splicing
+tools:
+  - "regtools":
+      description: "RegTools is a set of tools that integrate DNA-seq and RNA-seq data
+        to help interpret mutations in a regulatory and splicing context."
+      homepage: "https://regtools.readthedocs.io/en/latest/"
+      documentation: "https://regtools.readthedocs.io/en/latest/#usage"
+      tool_dev_url: "https://github.com/griffithlab/regtools"
+      licence: ["MIT"]
+      identifier: biotools:regtools
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - bam:
+        type: file
+        description: Sorted BAM file
+        pattern: "*.{bam}"
+    - bai:
+        type: file
+        description: Index to sorted BAM file
+        pattern: "*.{bai}"
+
+output:
+  - junc:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.junc":
+          type: file
+          description: |
+            BED12 file containing exon-exon "regtools_junctionsextract"
+          pattern: "*.{junc}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@abartlett004"
+maintainers:
+  - "@abartlett004"

modules/nf-core/regtools/junctionsextract/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process REGTOOLS_JUNCTIONSEXTRACT"
+    script "../main.nf"
+    process "REGTOOLS_JUNCTIONSEXTRACT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "regtools"
+    tag "regtools/junctionsextract"
+
+    test("homo_sapiens - bam-bai") {
+
+        when {
+            process {
+                """
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam.bai", checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - bam-bai - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam.bai", checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert snapshot(path(process.out.versions.get(0)).yaml).match("versions") }
+            )
+        }
+
+    }
+
+}

modules/nf-core/regtools/junctionsextract/tests/main.nf.test.snap

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+{
+    "homo_sapiens - bam-bai - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.junc:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,b8a1d662548217fc4607214fb7b4f42c"
+                ],
+                "junc": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.junc:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b8a1d662548217fc4607214fb7b4f42c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-20T13:29:27.373772"
+    },
+    "versions": {
+        "content": [
+            {
+                "REGTOOLS_JUNCTIONSEXTRACT": {
+                    "regtools": "0.5.0"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-20T13:29:27.448238"
+    },
+    "homo_sapiens - bam-bai": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.junc:md5,c0ccba2d76e9cb1588ba6d2e18c0742c"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,b8a1d662548217fc4607214fb7b4f42c"
+                ],
+                "junc": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.junc:md5,c0ccba2d76e9cb1588ba6d2e18c0742c"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b8a1d662548217fc4607214fb7b4f42c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-20T13:29:23.165022"
+    }
+}

modules/nf-core/regtools/junctionsextract/tests/tags.yml

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+regtools/junctionsextract:
+  - "modules/nf-core/regtools/junctionsextract/**"