new module wisecondorx/gender (#3333)

* new module wisecondorx/gender

* fix linting

modules/nf-core/wisecondorx/gender/main.nf

@@ -0,0 +1,47 @@
+process WISECONDORX_GENDER {
+    tag "$meta.id"
+    label 'process_low'
+
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+    conda "bioconda::wisecondorx=1.2.5"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/wisecondorx:1.2.5--pyh5e36f6f_0':
+        'quay.io/biocontainers/wisecondorx:1.2.5--pyh5e36f6f_0' }"
+
+    input:
+    tuple val(meta), path(npz)
+    tuple val(meta2), path(reference)
+
+    output:
+    tuple val(meta), stdout , emit: gender
+    path "versions.yml"     , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def VERSION = '1.2.5' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+
+    """
+    WisecondorX gender \\
+        ${npz} \\
+        ${reference}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        wisecondorx: ${VERSION}
+    END_VERSIONS
+    """
+
+    stub:
+    def VERSION = '1.2.5' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+
+    """
+    echo male
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        wisecondorx: ${VERSION}
+    END_VERSIONS
+    """
+}

modules/nf-core/wisecondorx/gender/meta.yml

@@ -0,0 +1,47 @@
+name: "wisecondorx_gender"
+description: Returns the gender of a .npz resulting from convert, based on a Gaussian mixture model trained during the newref phase
+keywords:
+  - copy number analysis
+  - gender determination
+  - npz
+tools:
+  - "wisecondorx":
+      description: "WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes"
+      homepage: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX"
+      documentation: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX"
+      tool_dev_url: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX"
+      doi: "10.1093/nar/gky1263"
+      licence: "['Attribution-NonCommercial-ShareAlike CC BY-NC-SA']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - npz:
+      type: file
+      description: Single sample NPZ file (from which to determine the gender)
+      pattern: "*.npz"
+  - reference:
+      type: file
+      description: Reference NPZ file
+      pattern: "*.npz"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - gender:
+      type: string
+      description: The gender of the input NPZ file
+      pattern: "(fe)?male"
+
+authors:
+  - "@nvnieuwk"

tests/config/pytest_modules.yml

@@ -3765,6 +3765,10 @@ wisecondorx/convert:
   - modules/nf-core/wisecondorx/convert/**
   - tests/modules/nf-core/wisecondorx/convert/**
 
+wisecondorx/gender:
+  - modules/nf-core/wisecondorx/gender/**
+  - tests/modules/nf-core/wisecondorx/gender/**
+
 wisecondorx/newref:
   - modules/nf-core/wisecondorx/newref/**
   - tests/modules/nf-core/wisecondorx/newref/**

tests/modules/nf-core/wisecondorx/gender/main.nf

@@ -0,0 +1,31 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { WISECONDORX_GENDER  } from '../../../../../modules/nf-core/wisecondorx/gender/main.nf'
+include { WISECONDORX_CONVERT } from '../../../../../modules/nf-core/wisecondorx/convert/main.nf'
+
+workflow test_wisecondorx_gender {
+
+    input = Channel.of([
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true)
+    ])
+
+    WISECONDORX_CONVERT(
+        input,
+        [[], []],
+        [[], []]
+    )
+
+    reference = [
+        [ id: "reference" ],
+        file("reference.npz")
+    ]
+
+    WISECONDORX_GENDER(
+        WISECONDORX_CONVERT.out.npz,
+        reference
+    )
+}

tests/modules/nf-core/wisecondorx/gender/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}

tests/modules/nf-core/wisecondorx/gender/test.yml

@@ -0,0 +1,7 @@
+- name: "wisecondorx gender"
+  command: nextflow run ./tests/modules/nf-core/wisecondorx/gender -entry test_wisecondorx_gender -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/wisecondorx/gender/nextflow.config -stub
+  tags:
+    - "wisecondorx"
+    - "wisecondorx/gender"
+  files:
+    - path: "output/wisecondorx/versions.yml"