feat: addition of vembrane table module

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

@@ -0,0 +1,49 @@
+
+
+process VEMBRANE_TABLE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/vembrane:2.4.0--pyhdfd78af_0':
+        'biocontainers/vembrane:2.4.0--pyhdfd78af_0'}"
+
+    input:
+    tuple val(meta), path(vcf)
+    val expression
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: table
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    vembrane table \\
+        $args \\
+        --output ${prefix}.tsv \\
+        '$expression' \\
+        $vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vembrane: \$(vembrane --version 2>&1 | head -n1 | sed 's/vembrane //')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vembrane: \$(vembrane --version 2>&1 | head -n1 | sed 's/vembrane //')
+    END_VERSIONS
+    """
+}

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

@@ -0,0 +1,63 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "vembrane_table"
+description: Creates tabular (TSV) files from VCF/BCF data with flexible Python expressions
+keywords:
+  - vcf
+  - bcf
+  - table
+  - genomics
+  - variant
+  - annotation
+tools:
+  - "vembrane":
+      description: "Filter VCF/BCF files with Python expressions"
+      homepage: "https://vembrane.github.io/"
+      documentation: "https://github.com/vembrane/vembrane/blob/main/docs/table.md"
+      tool_dev_url: "https://github.com/vembrane/vembrane"
+      doi: "10.1093/bioinformatics/btac810"
+      licence: ["MIT"]
+      identifier: biotools:vembrane
+      args_id: "$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 extract tabular data from
+        pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
+        ontologies:
+          - edam: http://edamontology.org/format_3016 # VCF
+  - expression:
+      type: string
+      description: A comma-separated tuple of expressions that define the table column contents
+
+output:
+  table:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.tsv":
+          type: file
+          description: TSV file containing tabular data from VCF/BCF
+          pattern: "*.tsv"
+          ontologies:
+            - edam: http://edamontology.org/format_3475 # TSV
+  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/table/tests/main.nf.test

@@ -0,0 +1,135 @@
+
+nextflow_process {
+
+    name "Test Process VEMBRANE_TABLE"
+    script "../main.nf"
+    process "VEMBRANE_TABLE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "vembrane"
+    tag "vembrane/table"
+
+    test("homo_sapiens - [vcf] - tsv") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
+                ]
+                input[1] = 'CHROM, POS, REF, ALT, QUAL'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - [bcf.gz] - tsv") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bcf.gz', checkIfExists: true)
+                ]
+                input[1] = 'CHROM, POS, REF, ALT, QUAL'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - [vcf] - csv - custom_separator") {
+
+        config "./nextflow.config"
+
+        when {
+            params {
+                vembrane_args = '--separator ,'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
+                ]
+                input[1] = 'CHROM, POS, REF, ALT'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - [vcf] - tsv - custom_header") {
+
+        config "./nextflow.config"
+
+        when {
+            params {
+                vembrane_args = '--header "Chromosome,Position,Variant_ID,Quality"'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
+                ]
+                input[1] = 'CHROM, POS, ID, QUAL'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - [vcf] - tsv - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
+                ]
+                input[1] = 'CHROM, POS, REF, ALT, QUAL'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}