New module: Whamg (#1994)

* added whamg

* linting

* linting

modules/whamg/main.nf

@@ -0,0 +1,41 @@
+process WHAMG {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::wham=1.8.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/wham:1.8.0.1.2017.05.03--h8b12597_1':
+        'quay.io/biocontainers/wham:1.8.0.1.2017.05.03--h8b12597_1' }"
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+    path(fasta)
+
+    output:
+    tuple val(meta), path("*.vcf.gz"), emit: vcf
+    path("*.txt")                    , emit: graph, optional: true
+    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}"
+
+    """
+    whamg \\
+        -x $task.cpus \\
+        -f $bam \\
+        -a $fasta \\
+        $args \\
+        > ${prefix}.vcf
+
+        gzip ${prefix}.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        whamg: \$(echo \$(whamg 2>&1 | grep Version | sed 's/^Version: v//; s/-.*\$//' ))
+    END_VERSIONS
+    """
+}

modules/whamg/meta.yml

@@ -0,0 +1,49 @@
+name: "whamg"
+description: The wham suite consists of two programs, wham and whamg. wham, the original tool, is a very sensitive method with a high false discovery rate. The second program, whamg, is more accurate and better suited for general structural variant (SV) discovery.
+keywords:
+  - whamg
+  - wham
+  - vcf
+  - bam
+  - variant calling
+tools:
+  - "whamg":
+      description: "Structural variant detection and association testing"
+      homepage: "https://github.com/zeeev/wham"
+      documentation: "https://github.com/zeeev/wham"
+      tool_dev_url: "https://github.com/zeeev/wham"
+      doi: "https://doi.org/10.1371/journal.pcbi.1004572"
+      licence: "['MIT']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM/SAM file
+      pattern: "*.{bam,sam}"
+  - bai:
+      type: file
+      description: BAM index file
+      pattern: "*.bai"
+
+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"
+  - vcf:
+      type: file
+      description: Compressed VCF file
+      pattern: "*.vcf.gz"
+
+authors:
+  - "@nvnieuwk"

tests/config/pytest_modules.yml

@@ -2332,6 +2332,10 @@ vsearch/usearchglobal:
   - modules/vsearch/usearchglobal/**
   - tests/modules/vsearch/usearchglobal/**
 
+whamg:
+  - modules/whamg/**
+  - tests/modules/whamg/**
+
 yara/index:
   - modules/yara/index/**
   - tests/modules/yara/index/**

tests/modules/whamg/main.nf

@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { WHAMG } from '../../../modules/whamg/main.nf'
+
+workflow test_whamg_bam {
+    
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    WHAMG ( input, fasta )
+}

tests/modules/whamg/nextflow.config

@@ -0,0 +1,8 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+    withName: WHAMG {
+        ext.args = ""
+    }
+}

tests/modules/whamg/test.yml

@@ -0,0 +1,6 @@
+- name: whamg test_whamg_bam
+  command: nextflow run ./tests/modules/whamg -entry test_whamg_bam -c ./tests/config/nextflow.config  -c ./tests/modules/whamg/nextflow.config
+  tags:
+    - whamg
+  files:
+    - path: output/whamg/test.vcf.gz