new module svtools/vcftobedpe (#7449)

* new module svtools/vcftobedpe * Update modules/nf-core/svtools/vcftobedpe/main.nf * Update modules/nf-core/svtools/vcftobedpe/main.nf Co-authored-by: James A. Fellows Yates <[email protected]> --------- Co-authored-by: James A. Fellows Yates <[email protected]>
nf-core · Feb 6, 2025 · 5cf15e4 · 5cf15e4
1 parent 1436029
commit 5cf15e4
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diff --git a/modules/nf-core/svtools/vcftobedpe/environment.yml b/modules/nf-core/svtools/vcftobedpe/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::svtools=0.5.1"
diff --git a/modules/nf-core/svtools/vcftobedpe/main.nf b/modules/nf-core/svtools/vcftobedpe/main.nf
@@ -0,0 +1,46 @@
+process SVTOOLS_VCFTOBEDPE {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/svtools:0.5.1--py_0':
+        'biocontainers/svtools:0.5.1--py_0' }"
+
+    input:
+    tuple val(meta), path(vcf)
+
+    output:
+    tuple val(meta), path("*.bedpe"), emit: bedpe
+    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}"
+    """
+    svtools vcftobedpe \\
+        $args
+        --input $vcf \\
+        --output ${prefix}.bedpe \\
+        --tempdir ./tmp
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        svtools: \$(svtools --version |& sed '1!d ; s/svtools //')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bedpe
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        svtools: \$(svtools --version |& sed '1!d ; s/svtools //')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/svtools/vcftobedpe/meta.yml b/modules/nf-core/svtools/vcftobedpe/meta.yml
@@ -0,0 +1,49 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "svtools_vcftobedpe"
+description: Convert a VCF file to a BEDPE file.
+keywords:
+  - structural
+  - bedpe
+  - vcf
+  - conversion
+  - variants
+tools:
+  - "svtools":
+      description: "Tools for processing and analyzing structural variants"
+      tool_dev_url: "https://github.com/hall-lab/svtools"
+      licence: ['MIT License']
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - vcf:
+        type: file
+        description: Input VCF file containing structural variants
+        pattern: "*.{vcf,vcf.gz}"
+
+output:
+  - bedpe:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - "*.bedpe":
+        type: file
+        description: The converted BEDPE file
+        pattern: "*.bedpe"
+
+  - versions:
+    - "versions.yml":
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+
+authors:
+  - "@nvnieuwk"
+maintainers:
+  - "@nvnieuwk"
diff --git a/modules/nf-core/svtools/vcftobedpe/tests/main.nf.test b/modules/nf-core/svtools/vcftobedpe/tests/main.nf.test
@@ -0,0 +1,58 @@
+nextflow_process {
+
+    name "Test Process SVTOOLS_VCFTOBEDPE"
+    script "../main.nf"
+    process "SVTOOLS_VCFTOBEDPE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "svtools"
+    tag "svtools/vcftobedpe"
+
+    test("homo_sapiens - vcf") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - vcf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/svtools/vcftobedpe/tests/main.nf.test.snap b/modules/nf-core/svtools/vcftobedpe/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "homo_sapiens - vcf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bedpe:md5,78e3231e39d534d26ba32f64f8f5e094"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,1af4f5a32bfc89f4d6d6c94cf1d4afd8"
+                ],
+                "bedpe": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bedpe:md5,78e3231e39d534d26ba32f64f8f5e094"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,1af4f5a32bfc89f4d6d6c94cf1d4afd8"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-06T16:08:14.1286306"
+    },
+    "homo_sapiens - vcf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bedpe:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,1af4f5a32bfc89f4d6d6c94cf1d4afd8"
+                ],
+                "bedpe": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bedpe:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,1af4f5a32bfc89f4d6d6c94cf1d4afd8"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-06T16:08:21.008497589"
+    }
+}