Newmodule ngmerge (#3626)

* ngmerge first commit

* main module code

* complete module

* remove trailing whitespace

* fix versions.yml

* fix version yml

* versions yml

* vyml

* try vyml again

* touch versions yml

* vyml

modules/nf-core/ngmerge/main.nf

@@ -0,0 +1,52 @@
+process NGMERGE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "bioconda::ngmerge=0.3"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ngmerge:0.3--ha92aebf_1':
+        'biocontainers/ngmerge:0.3--ha92aebf_1' }"
+
+    input:
+    tuple val(meta), path(reads1), path(reads2)
+
+    output:
+    tuple val(meta), path("*.merged.fq.gz"), emit: merged_reads
+    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}"
+
+    """
+    NGmerge \\
+        -1 $reads1 \\
+        -2 $reads2 \\
+        -o ${prefix}.merged.fq.gz \\
+        -z \\
+        -n $task.cpus \\
+        $args
+
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        NGmerge: \$(echo \$(NGmerge --version 2>&1) | sed 's/^.*NGmerge, version //; s/ Copyright.*// ; s/: //g' ))
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}.merged.fq.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        NGmerge: \$(echo \$(NGmerge --version 2>&1) | sed 's/^.*NGmerge, version //; s/ Copyright.*// ; s/: //g' ))
+    END_VERSIONS
+    """
+}

modules/nf-core/ngmerge/meta.yml

@@ -0,0 +1,54 @@
+---
+name: "ngmerge"
+
+description: Merging paired-end reads and removing sequencing adapters.
+keywords:
+  - sort
+  - reads merging
+  - merge mate pairs
+tools:
+  - "ngmerge":
+      description: "Merging paired-end reads and removing sequencing adapters."
+      homepage: "https://github.com/jsh58/NGmerge"
+      documentation: "https://github.com/jsh58/NGmerge"
+      tool_dev_url: "https://github.com/jsh58/NGmerge"
+      doi: "10.1186/s12859-018-2579-2"
+      licence: "['MIT']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - reads1:
+      type: file
+      description: fastq file paired end read 1
+      pattern: "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}"
+
+  - reads2:
+      type: file
+      description: fastq file paired end read 2
+      pattern: "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}"
+
+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"
+
+  - merged_reads:
+      type: file
+      description: fastq file paired end read 2
+      pattern: "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}"
+
+authors:
+  - "@charlotteanne"
+  - "@jsh58"

tests/config/pytest_modules.yml

@@ -2531,6 +2531,10 @@ ngmaster:
   - modules/nf-core/ngmaster/**
   - tests/modules/nf-core/ngmaster/**
 
+ngmerge:
+  - modules/nf-core/ngmerge/**
+  - tests/modules/nf-core/ngmerge/**
+
 ngsbits/samplegender:
   - modules/nf-core/ngsbits/samplegender/**
   - tests/modules/nf-core/ngsbits/samplegender/**

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

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { NGMERGE } from '../../../../modules/nf-core/ngmerge/main.nf'
+
+workflow test_ngmerge {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)],
+        [ file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)]
+    ]
+
+    NGMERGE ( input )
+}

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

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

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

@@ -0,0 +1,7 @@
+- name: ngmerge test_ngmerge
+  command: nextflow run ./tests/modules/nf-core/ngmerge -entry test_ngmerge -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ngmerge/nextflow.config
+  tags:
+    - ngmerge
+  files:
+    - path: output/ngmerge/test.merged.fq.gz
+    - path: output/ngmerge/versions.yml