New module echtvar/encode

modules/nf-core/echtvar/encode/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::echtvar=0.2.4"

modules/nf-core/echtvar/encode/main.nf

@@ -0,0 +1,41 @@
+process ECHTVAR_ENCODE {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87b75cb9e32b89261e8cbdca40b219a5d58fc78ebf92d5ca97c7ca23da1b9517/data':
+        'community.wave.seqera.io/library/echtvar:0.2.4--e59eba33636e3aab' }"
+
+    input:
+    tuple val(meta), path(vcf)
+    tuple val(meta2), path(json_filters)
+
+    output:
+    tuple val(meta), path("*.zip"), emit: db
+    tuple val("${task.process}"), val('echtvar'), eval("echtvar --version | sed 's/echtvar //g'"), emit: versions_echtvar, topic: versions 
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echtvar \\
+        encode \\
+        $args \\
+        ${prefix}.zip \\
+        ${json_filters} \\
+        $vcf
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo $args
+
+    touch ${prefix}.zip
+    """
+}

modules/nf-core/echtvar/encode/meta.yml

@@ -0,0 +1,79 @@
+name: "echtvar_encode"
+description: Make (encode) a new echtvar file from decomposed vcf
+keywords:
+  - vcf
+  - echtvar
+  - encode
+  - annotation
+  - allele-frequency
+tools:
+  - "echtvar":
+      description: "Using all the bits for echt rapid variant annotation and filtering."
+      homepage: "https://github.com/brentp/echtvar/blob/v0.2.2/README.md"
+      documentation: "https://github.com/brentp/echtvar/blob/v0.2.2/README.md"
+      tool_dev_url: "https://github.com/brentp/echtvar"
+      doi: "10.1093/nar/gkac931"
+      licence:
+        - "MIT"
+      identifier: biotools:echtvar
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - vcf:
+        type: file
+        description: VCF file
+        pattern: "*.vcf"
+        ontologies:
+          - edam: "http://edamontology.org/format_3016"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - json_filters:
+        type: file
+        description: JSON file containing the configuration for the encoding process (which columns are pulled from the input VCF and how they are stored)
+        pattern: "*.json"
+        ontologies:
+          - edam: "http://edamontology.org/format_3464"
+output:
+  db:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.zip":
+          type: file
+          description: Encoded ECHTVAR file
+          pattern: "*.zip"
+          ontologies:
+            - edam: "http://edamontology.org/format_3987"
+  versions_echtvar:
+    - - "${task.process}":
+          type: string
+          description: The name of the process
+      - "echtvar":
+          type: string
+          description: The name of the tool
+      - "echtvar --version | sed 's/echtvar //g'":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - "${task.process}":
+          type: string
+          description: The name of the process
+      - "echtvar":
+          type: string
+          description: The name of the tool
+      - "echtvar --version | sed 's/echtvar //g'":
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@sofiademmou"
+maintainers:
+  - "@sofiademmou"

modules/nf-core/echtvar/encode/tests/main.nf.test

@@ -0,0 +1,93 @@
+nextflow_process {
+
+    name "Test Process ECHTVAR_ENCODE"
+    script "../main.nf"
+    process "ECHTVAR_ENCODE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "echtvar"
+    tag "echtvar/encode"
+    tag "bcftools/norm"
+
+    config "./nextflow.config"
+
+    setup {
+        run("BCFTOOLS_NORM") {
+            script "../../../bcftools/norm/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true),
+                    []
+                ]
+                input[1] = [
+                    [ id:'genome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.gz', checkIfExists: true)
+                ]
+            """
+            }
+        }
+    }
+
+    test("homo_sapiens - vcf") {
+
+        when {
+            process {
+                """
+                // Create dummy json config file for testing
+                def json_config = file("${moduleDir}/tests/config.json")
+                json_config.text = '[{"field": "DP", "alias": "gnomad_dp"}]'
+
+                input[0] = BCFTOOLS_NORM.out.vcf
+
+                input[1] = [
+                    [ id:'test_db' ],
+                    file(json_config)
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    sanitizeOutput(process.out)
+                ).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - vcf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                // Create dummy json config file for testing
+                def json_config = file("${moduleDir}/tests/config.json")
+                json_config.text = '[{"field": "DP", "alias": "gnomad_dp"}]'
+
+                input[0] = BCFTOOLS_NORM.out.vcf
+
+                input[1] = [
+                    [ id:'test_db' ],
+                    file(json_config)
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    sanitizeOutput(process.out)
+                ).match() }
+            )
+        }
+    }
+}

modules/nf-core/echtvar/encode/tests/main.nf.test.snap

@@ -0,0 +1,54 @@
+{
+    "homo_sapiens - vcf": {
+        "content": [
+            {
+                "db": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.zip:md5,0c0f642e4c77b2ae78484c915fbe47a1"
+                    ]
+                ],
+                "versions_echtvar": [
+                    [
+                        "ECHTVAR_ENCODE",
+                        "echtvar",
+                        "0.2.4"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-06-18T14:42:59.497378002",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.4"
+        }
+    },
+    "homo_sapiens - vcf - stub": {
+        "content": [
+            {
+                "db": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_echtvar": [
+                    [
+                        "ECHTVAR_ENCODE",
+                        "echtvar",
+                        "0.2.4"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-06-18T14:43:04.351665131",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.4"
+        }
+    }
+}

modules/nf-core/echtvar/encode/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: "BCFTOOLS_NORM" {
+        ext.args = ' -m - -w 10000 -O b '
+    }
+}