New module: wgsim (#2178)

module wgsim

modules/nf-core/wgsim/main.nf

@@ -0,0 +1,36 @@
+process WGSIM {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::wgsim=1.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/wgsim:1.0--h5bf99c6_4':
+        'quay.io/biocontainers/wgsim:1.0--h5bf99c6_4' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.fastq"), emit: fastq
+    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 WGSIM_VERSION = "0.3.1-r13" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    wgsim \\
+        $args \\
+        $fasta \\
+        ${prefix}_1.fastq ${prefix}_2.fastq
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        wgsim: $WGSIM_VERSION
+    END_VERSIONS
+    """
+}

modules/nf-core/wgsim/meta.yml

@@ -0,0 +1,43 @@
+name: "wgsim"
+description: simulating sequence reads from a reference genome
+keywords:
+  - simulate
+  - fasta
+  - reads
+tools:
+  - "wgsim":
+      description: "simulating sequence reads from a reference genome"
+      homepage: "https://github.com/lh3/wgsim"
+      documentation: "https://github.com/lh3/wgsim"
+      tool_dev_url: "https://github.com/lh3/wgsim"
+      doi: ""
+      licence: "['MIT']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: Genome fasta file
+      pattern: "*.{fa,fasta}"
+
+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"
+  - fastq:
+      type: file
+      description: Simulated FASTQ read files
+      pattern: "*.{fastq}"
+
+authors:
+  - "@priyanka-surana"

tests/config/pytest_modules.yml

@@ -2540,6 +2540,10 @@ vsearch/usearchglobal:
   - modules/nf-core/vsearch/usearchglobal/**
   - tests/modules/nf-core/vsearch/usearchglobal/**
 
+wgsim:
+  - modules/nf-core/wgsim/**
+  - tests/modules/nf-core/wgsim/**
+
 whamg:
   - modules/nf-core/whamg/**
   - tests/modules/nf-core/whamg/**

tests/modules/nf-core/wgsim/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { WGSIM } from '../../../../modules/nf-core/wgsim/main.nf'
+
+workflow test_wgsim {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    WGSIM ( input )
+}

tests/modules/nf-core/wgsim/nextflow.config

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

tests/modules/nf-core/wgsim/test.yml

@@ -0,0 +1,7 @@
+- name: wgsim test_wgsim
+  command: nextflow run ./tests/modules/nf-core/wgsim -entry test_wgsim -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/wgsim/nextflow.config
+  tags:
+    - wgsim
+  files:
+    - path: output/wgsim/test_1.fastq
+    - path: output/wgsim/test_2.fastq