New Module: NextGenMap (#1938)

adding nextgenmap module

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

modules/nextgenmap/main.nf

@@ -0,0 +1,58 @@
+process NEXTGENMAP {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::nextgenmap=0.5.5" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/nextgenmap%3A0.5.5--hc9558a2_4' :
+        'quay.io/biocontainers/nextgenmap:0.5.5--hc9558a2_4' }"
+
+    input:
+    tuple val(meta), path(reads)
+    path(fasta)
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    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 threads = task.cpus
+
+    if(meta.single_end){
+        """
+        ngm \\
+            -r $fasta \\
+            -q $reads \\
+            -t $threads \\
+            --bam \\
+            -o ${prefix}.bam \\
+            $args
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            NextGenMap: \$(ngm 2>&1 | head -1 | grep -o -E '[[:digit:]]+.[[:digit:]]+.[[:digit:]]+')
+        END_VERSIONS
+        """
+    } else{
+        """
+        ngm \\
+            -r $fasta \\
+            -1 ${reads[0]} \\
+            -2 ${reads[1]} \\
+            -t $threads \\
+            --bam \\
+            -o ${prefix}.bam \\
+            $args
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            NextGenMap: \$(ngm 2>&1 | head -1 | grep -o -E '[[:digit:]]+.[[:digit:]]+.[[:digit:]]+')
+        END_VERSIONS
+        """
+    }
+}

modules/nextgenmap/meta.yml

@@ -0,0 +1,55 @@
+name: nextgenmap
+description: Performs fastq alignment to a fasta reference using NextGenMap
+keywords:
+  - NextGenMap
+  - ngm
+  - alignment
+  - map
+  - fastq
+  - bam
+  - sam
+tools:
+  - bwa:
+      description: |
+        NextGenMap is a flexible highly sensitive short read mapping tool that
+        handles much higher mismatch rates than comparable algorithms while
+        still outperforming them in terms of runtime
+      homepage: https://github.com/Cibiv/NextGenMap
+      documentation: https://github.com/Cibiv/NextGenMap/wiki
+      doi: 10.1093/bioinformatics/btt468
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: |
+        List of input FastQ files of size 1, if meta.single_end is true, and 2
+        if meta.single_end is false.
+  - fasta:
+      type: file
+      description: |
+        Genomic reference fasta file
+      pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information. First item of tuple with
+        bam, below.
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: |
+        Output BAM file containing read alignments. Second item of tuple with
+        meta, above
+      pattern: "*.{bam}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@cmatkhan"

tests/config/pytest_modules.yml

@@ -1723,6 +1723,10 @@ nextclade/run:
   - modules/nextclade/run/**
   - tests/modules/nextclade/run/**
 
+nextgenmap:
+  - modules/nextgenmap/**
+  - tests/modules/nextgenmap/**
+
 ngmaster:
   - modules/ngmaster/**
   - tests/modules/ngmaster/**

tests/modules/nextgenmap/main.nf

@@ -0,0 +1,36 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { NEXTGENMAP } from '../../../modules/nextgenmap/main.nf'
+
+//
+// Test with single-end data
+//
+workflow test_nextgenmap_single {
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    NEXTGENMAP ( input, fasta )
+}
+
+//
+// Test with paired-end data
+//
+workflow test_bwamem2_mem_paired_end {
+    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)
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    NEXTGENMAP ( input, fasta )
+}

tests/modules/nextgenmap/nextflow.config

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

tests/modules/nextgenmap/test.yml

@@ -0,0 +1,15 @@
+- name: nextgenmap test_nextgenmap_single
+  command: nextflow run ./tests/modules/nextgenmap -entry test_nextgenmap_single -c ./tests/config/nextflow.config  -c ./tests/modules/nextgenmap/nextflow.config
+  tags:
+    - nextgenmap
+  files:
+    - path: output/nextgenmap/test.bam
+      md5sum: ada069bc5c670ffee23871f3ca525d0a
+
+- name: nextgenmap test_bwamem2_mem_paired_end
+  command: nextflow run ./tests/modules/nextgenmap -entry test_bwamem2_mem_paired_end -c ./tests/config/nextflow.config  -c ./tests/modules/nextgenmap/nextflow.config
+  tags:
+    - nextgenmap
+  files:
+    - path: output/nextgenmap/test.bam
+      md5sum: fa76167e236cf1aabdafdbb0632253cd