New Module: Octopusv/correct

modules/nf-core/octopusv/correct/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::octopusv=0.3.2"

modules/nf-core/octopusv/correct/main.nf

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+process OCTOPUSV_CORRECT {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/octopusv:0.3.2--pyhdfd78af_0' :
+        'quay.io/biocontainers/octopusv:0.3.2--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(vcf)
+
+    output:
+    tuple val(meta), path("*.svcf"), emit: svcf
+    tuple val("${task.process}"), val('octopusv'), eval("octopusv --version"), emit: versions_octopusv, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    octopusv correct \\
+        -i ${vcf} \\
+        -o ${prefix}.svcf \\
+        $args
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    echo $args
+
+    touch ${prefix}.svcf
+    """
+}

modules/nf-core/octopusv/correct/meta.yml

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+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "octopusv_correct"
+description: "Standardize a caller VCF into OctopuSV SVCF format."
+keywords:
+  - structural
+  - variant
+  - sv
+  - svcf
+  - normalize
+tools:
+  - "octopusv":
+      description: "End-to-end structural variant post-processing: standardize, merge, compare, and export SVs."
+      homepage: "https://github.com/ylab-hi/OctopuSV"
+      documentation: "https://github.com/ylab-hi/OctopuSV"
+      tool_dev_url: "https://github.com/ylab-hi/OctopuSV"
+      doi: "10.1093/bioinformatics/btaf599"
+      licence: ["MIT"]
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - vcf:
+        type: file
+        description: Structural variant calls in VCF format
+        pattern: "*.{vcf,vcf.gz}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3016" # VCF
+output:
+  svcf:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+      - "*.svcf":
+          type: file
+          description: Standardized SVCF file
+          pattern: "*.svcf"
+          ontologies:
+            - edam: "https://github.com/ylab-hi/OctopuSV/blob/main/docs/SVCF_specifications.md" # SVCF
+  versions_octopusv:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - octopusv:
+          type: string
+          description: The name of the tool
+      - octopusv --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - octopusv:
+          type: string
+          description: The name of the tool
+      - octopusv --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@manascripts"
+maintainers:
+  - "@manascripts"

modules/nf-core/octopusv/correct/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process OCTOPUSV_CORRECT"
+    script "../main.nf"
+    process "OCTOPUSV_CORRECT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "octopusv"
+    tag "octopusv/correct"
+
+    test("homo_sapiens - vcf") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + '.../data/genomics/homo_sapiens/illumina/vcf/gridss.somatic.vcf', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.svcf.get(0).get(1)).name,
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - vcf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + '.../data/genomics/homo_sapiens/illumina/vcf/gridss.somatic.vcf', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+
+    }
+
+}