feat: BCFTOOLS_PLUGINVCF2TABLE

modules/nf-core/bcftools/pluginvcf2table/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::bcftools=1.23.1"

modules/nf-core/bcftools/pluginvcf2table/main.nf

@@ -0,0 +1,45 @@
+process BCFTOOLS_PLUGINVCF2TABLE {
+    tag "${meta.id}"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'oras://community.wave.seqera.io/library/bcftools:1.23.1--16b1a31e5dc795f7'
+        : 'community.wave.seqera.io/library/bcftools:1.23.1--4d193a5f61d4aed7'}"
+
+    input:
+    tuple val(meta), path(vcf), path(tbi)
+    tuple val(meta2), path(regions)
+    tuple val(meta3), path(targets)
+    tuple val(meta4), path(samples)
+
+    output:
+    tuple val(meta), path("*.txt"), emit: txt
+    tuple val("${task.process}"), val('bcftools'), eval("bcftools --version"), topic: versions, emit: versions_bcftools
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def regions_file = regions ? "--regions-file ${regions}" : ''
+    def targets_file = targets ? "--targets-file ${targets}" : ''
+    def samples_file = samples ? "--samples-file ${samples}" : ''
+    """
+    bcftools \\
+        +vcf2table \\
+        ${args} \\
+        ${regions_file} \\
+        ${targets_file} \\
+        ${samples_file} \\
+        ${vcf} \\
+        > ${prefix}.txt
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.txt
+    """
+}

modules/nf-core/bcftools/pluginvcf2table/meta.yml

@@ -0,0 +1,119 @@
+name: bcftools_pluginvcf2table
+description: |
+  Converts VCF/BCF files into a tab-delimited table using the bcftools +vcf2table plugin.
+  Each variant is output as one row, with INFO and FORMAT fields as columns.
+keywords:
+  - bcftools
+  - vcf
+  - table
+  - variant calling
+tools:
+  - bcftools:
+      description: |
+        BCFtools is a set of utilities for variant calling and manipulating VCF/BCF files.
+        The +vcf2table plugin converts VCF records into a tab-delimited table format.
+      homepage: http://samtools.github.io/bcftools/bcftools.html
+      documentation: http://www.htslib.org/doc/bcftools.html
+      doi: "10.1093/gigascience/giab008"
+      licence:
+        - "MIT"
+      identifier: biotools:bcftools
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+        ontologies: []
+    - vcf:
+        type: file
+        description: VCF/BCF file to be converted (optionally bgzipped).
+        pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3016" # VCF
+    - tbi:
+        type: file
+        description: Index of the VCF/BCF file (required when vcf is bgzipped).
+        pattern: "*.{tbi,csi}"
+        ontologies: []
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing regions file information
+          e.g. [ id:'test' ]
+        ontologies: []
+    - regions:
+        type: file
+        description: |
+          Optional. Restrict the operation to regions listed in this BED or VCF file.
+          Relies on a tabix index.
+        pattern: "*.{bed,vcf,vcf.gz}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3003" # BED
+          - edam: "http://edamontology.org/format_3016" # VCF
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing targets file information
+          e.g. [ id:'test' ]
+        ontologies: []
+    - targets:
+        type: file
+        description: |
+          Optional. Restrict the operation to regions listed in this file
+          (does not rely on index files).
+        pattern: "*.{bed,vcf,vcf.gz}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3003" # BED
+          - edam: "http://edamontology.org/format_3016" # VCF
+  - - meta4:
+        type: map
+        description: |
+          Groovy Map containing samples file information
+          e.g. [ id:'test' ]
+        ontologies: []
+    - samples:
+        type: file
+        description: |
+          Optional. File of sample names to include or exclude.
+        pattern: "*.txt"
+        ontologies: []
+output:
+  txt:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+          ontologies: []
+      - "*.txt":
+          type: file
+          description: Tab-delimited table output from bcftools +vcf2table.
+          pattern: "*.txt"
+          ontologies:
+            - edam: "http://edamontology.org/format_3475" # TSV
+  versions_bcftools:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - bcftools:
+          type: string
+          description: The name of the tool
+      - "bcftools --version":
+          type: string
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - bcftools:
+          type: string
+          description: The name of the tool
+      - "bcftools --version":
+          type: string
+          description: The expression to obtain the version of the tool
+authors:
+  - "@emmcauley"
+maintainers:
+  - "@emmcauley"

modules/nf-core/bcftools/pluginvcf2table/tests/main.nf.test

@@ -0,0 +1,119 @@
+nextflow_process {
+
+    name "Test Process BCFTOOLS_PLUGINVCF2TABLE"
+    script "../main.nf"
+    process "BCFTOOLS_PLUGINVCF2TABLE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bcftools"
+    tag "bcftools/pluginvcf2table"
+
+    test("homo_sapiens - vcf_gz - tbi") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    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)
+                ]
+                input[1] = [ [], [] ]
+                input[2] = [ [], [] ]
+                input[3] = [ [], [] ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() },
+            )
+        }
+
+    }
+
+    test("homo_sapiens - vcf_gz - tbi - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    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)
+                ]
+                input[1] = [ [], [] ]
+                input[2] = [ [], [] ]
+                input[3] = [ [], [] ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() },
+            )
+        }
+
+
+    }
+    test("homo_sapiens - vcf_gz - tbi - regions") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    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)
+                ]
+                input[1] = [ ['test_regions'], [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bed/test.bed', checkIfExists: true) ] ]
+                input[2] = [ [], [] ]
+                input[3] = [ [], [] ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() },
+            )
+        }
+
+    }
+
+    test("homo_sapiens - vcf_gz - tbi - regions - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    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)
+                ]
+                input[1] = [ ['test_regions'], [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bed/test.bed', checkIfExists: true) ] ]
+                input[2] = [ [], [] ]
+                input[3] = [ [], [] ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() },
+            )
+        }
+
+    }
+}