add new module vt/decompose_blocksub

modules/nf-core/vt/decomposeblocksub/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::vt=2015.11.10"

modules/nf-core/vt/decomposeblocksub/main.nf

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+process VT_DECOMPOSEBLOCKSUB {
+    tag "$meta.id"
+    label 'process_low'
+
+    // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/vt:2015.11.10--h5ef6573_4':
+        'biocontainers/vt:2015.11.10--h5ef6573_4' }"
+
+    input:
+    tuple val(meta), path(vcf), path(index), path(intervals)
+
+    output:
+    tuple val(meta), path("*.vcf.gz")   , emit: vcf
+    path "versions.yml"                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    if ("$vcf" == "${prefix}.vcf.gz") {
+        error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+    }
+
+    def bed = intervals ? "-i ${intervals}" : ""
+    """
+    vt decompose_blocksub \\
+        -o ${prefix}.vcf.gz \\
+        ${bed} \\
+        ${args} \\
+        ${vcf}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vt: \$(echo \$(vt decompose_blocksub 2>&1 | grep 'decompose_blocksub v' | sed -n 's/.*decompose_blocksub v\\([0-9]\\+\\.[0-9]\\+\\).*/\\1/p' ))
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    if ("$vcf" == "${prefix}.vcf.gz") {
+        error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+    }
+
+    """
+    touch ${prefix}.vcf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vt: \$(echo \$(vt decompose_blocksub 2>&1 | grep 'decompose_blocksub v' | sed -n 's/.*decompose_blocksub v\\([0-9]\\+\\.[0-9]\\+\\).*/\\1/p' ))
+    END_VERSIONS
+    """
+}

modules/nf-core/vt/decomposeblocksub/meta.yml

@@ -0,0 +1,63 @@
+name: "vt_decomposeblocksub"
+description: Decomposes biallelic block substitutions into its constituent SNPs.
+keywords:
+  - decomposeblocksub
+  - multiallelic
+  - small variants
+  - snps
+  - indels
+  - block substitutions
+tools:
+  - "vt":
+      description: "A tool set for short variant discovery in genetic sequence data"
+      homepage: "https://genome.sph.umich.edu/wiki/Vt"
+      documentation: "https://genome.sph.umich.edu/wiki/Vt"
+      tool_dev_url: "https://github.com/atks/vt"
+      licence: ["MIT"]
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'test', single_end:false ]`
+    - vcf:
+        type: file
+        description: The VCF file to decompose
+        pattern: "*.vcf(.gz)?"
+        ontologies:
+          - edam: "http://edamontology.org/format_3016"
+    - index:
+        type: file
+        description: The VCF file to decompose
+        pattern: "*.tbi"
+        ontologies:
+          - edam: "http://edamontology.org/format_3616"
+    - intervals:
+        type: file
+        description: The intervals of the variants of decompose
+        pattern: "*.bed"
+        ontologies:
+          - edam: "http://edamontology.org/format_3003"
+output:
+  - vcf:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*.vcf.gz":
+          type: file
+          description: The decomposed VCF file
+          pattern: "*.vcf.gz"
+          ontologies:
+          - edam: "http://edamontology.org/format_3016"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@kubranarci"
+maintainers:
+  - "@kubranarci"

modules/nf-core/vt/decomposeblocksub/tests/main.nf.test

@@ -0,0 +1,62 @@
+
+nextflow_process {
+
+    name "Test Process VT_DECOMPOSEBLOCKSUB"
+    script "../main.nf"
+    process "VT_DECOMPOSEBLOCKSUB"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "vt"
+    tag "vt/decomposeblocksub"
+
+    test("test-vt-decomposeblocksub") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
+				[]
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-vt-decomposeblocksub-intervals") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				[ id:'test', single_end:false ], // meta map
+				file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true),
+                [],
+				file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/vt/decomposeblocksub/tests/main.nf.test.snap

@@ -0,0 +1,72 @@
+{
+    "test-vt-decomposeblocksub-intervals": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "decomposeblocksub.vcf.gz:md5,6dd85c7989b945dccb0a834c2c05407a"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,2e541ec639f0458804a6cd3a58211f66"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "decomposeblocksub.vcf.gz:md5,6dd85c7989b945dccb0a834c2c05407a"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2e541ec639f0458804a6cd3a58211f66"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-03T09:38:47.060601884"
+    },
+    "test-vt-decomposeblocksub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "decomposeblocksub.vcf.gz:md5,6dd85c7989b945dccb0a834c2c05407a"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,2e541ec639f0458804a6cd3a58211f66"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "decomposeblocksub.vcf.gz:md5,6dd85c7989b945dccb0a834c2c05407a"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2e541ec639f0458804a6cd3a58211f66"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-03T09:38:24.537448596"
+    }
+}

modules/nf-core/vt/decomposeblocksub/tests/nextflow.config

@@ -0,0 +1,6 @@
+process {
+    withName: VT_DECOMPOSEBLOCKSUB {
+        ext.prefix = "decomposeblocksub"
+        ext.args   = "-a"
+    }
+}