feat: addition of vembrane sort module

modules/nf-core/vembrane/sort/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::vembrane=2.4.0

modules/nf-core/vembrane/sort/main.nf

@@ -0,0 +1,58 @@
+process VEMBRANE_SORT {
+    tag "${meta.id}"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/vembrane:2.4.0--pyhdfd78af_0'
+        : 'biocontainers/vembrane:2.4.0--pyhdfd78af_0'}"
+
+    input:
+    tuple val(meta), path(vcf)
+    val expression
+
+    output:
+    tuple val(meta), path("*.vcf*"), emit: vcf
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix = args.contains('--output-fmt vcf.gz')
+        ? 'vcf.gz'
+        : args.contains('--output-fmt bcf')
+            ? 'bcf'
+            : args.contains('--output-fmt bcf.gz') ? 'bcf.gz' : 'vcf'
+    """
+    vembrane sort \\
+        ${args} \\
+        --output ${prefix}.${suffix} \\
+        '${expression}' \\
+        ${vcf}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vembrane: \$(vembrane --version 2>&1 | head -n1 | sed 's/vembrane //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix = args.contains('--output-fmt vcf.gz')
+        ? 'vcf.gz'
+        : args.contains('--output-fmt bcf')
+            ? 'bcf'
+            : args.contains('--output-fmt bcf.gz') ? 'bcf.gz' : 'vcf'
+    """
+    touch ${prefix}.${suffix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vembrane: \$(vembrane --version 2>&1 | head -n1 | sed 's/vembrane //')
+    END_VERSIONS
+    """
+}

modules/nf-core/vembrane/sort/meta.yml

@@ -0,0 +1,63 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "vembrane_sort"
+description: Sort VCF/BCF files by custom Python expressions for variant prioritization
+keywords:
+  - vcf
+  - bcf
+  - sort
+  - genomics
+  - variant
+  - prioritization
+tools:
+  - "vembrane":
+      description: "Filter VCF/BCF files with Python expressions"
+      homepage: "https://vembrane.github.io/"
+      documentation: "https://github.com/vembrane/vembrane/blob/main/docs/sort.md"
+      tool_dev_url: "https://github.com/vembrane/vembrane"
+      doi: "10.1093/bioinformatics/btac810"
+      licence: ["MIT"]
+      identifier: biotools:vembrane
+      args_id: "$args"
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - vcf:
+        type: file
+        description: VCF/BCF file to sort
+        pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
+        ontologies:
+          - edam: http://edamontology.org/format_3016 # VCF
+  - expression:
+      type: string
+      description: Python expression (or tuple of expressions) returning orderable values to sort by
+
+output:
+  vcf:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.vcf*":
+          type: file
+          description: Sorted VCF file (can be compressed)
+          pattern: "*.{vcf,vcf.gz}"
+          ontologies:
+            - edam: http://edamontology.org/format_3016 # VCF
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+authors:
+- "@mkatsanto"
+- "@trangdo-hsc"
+maintainers:
+- "@mkatsanto"
+- "@trangdo-hsc"

modules/nf-core/vembrane/sort/tests/main.nf.test

@@ -0,0 +1,181 @@
+nextflow_process {
+
+    name "Test Process VEMBRANE_SORT"
+    script "../main.nf"
+    process "VEMBRANE_SORT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "vembrane"
+    tag "vembrane/sort"
+
+    test("homo_sapiens - [vcf] - vcf - quality_sort") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
+                ]
+                input[1] = 'QUAL'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - [vcf] - vcf - position_sort") {
+
+        config "./nextflow.config"
+
+        when {
+            params {
+                vembrane_args = '--output-fmt vcf'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
+                ]
+                input[1] = 'CHROM, POS'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - [vcf] - vcf - descending_sort") {
+
+        config "./nextflow.config"
+
+        when {
+            params {
+                vembrane_args = '--preserve-annotation-order'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
+                ]
+                input[1] = 'desc(QUAL)'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - [vcf] - vcf - depth_sort") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_depth' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
+                ]
+                input[1] = 'INFO["DP"] if "DP" in INFO else 0'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - [vcf] - vcf - numeric_expression") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_numeric' ], // meta map  
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
+                ]
+                input[1] = 'POS % 1000'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - [vcf] - vcf - multi_field_sort") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_multi' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
+                ]
+                input[1] = '(CHROM, POS, QUAL)'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - [vcf] - vcf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_stub' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
+                ]
+                input[1] = 'QUAL'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
+    }
+
+}