Merge branch 'master' into biobambam/bammerge

modules/hmtnote/main.nf

@@ -0,0 +1,45 @@
+process HMTNOTE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::hmtnote=0.7.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/hmtnote:0.7.2--pyhdfd78af_0':
+        'quay.io/biocontainers/hmtnote:0.7.2--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(vcf)
+
+    output:
+    tuple val(meta), path("*_annotated.vcf"), emit: vcf
+    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}"
+
+    """
+    hmtnote \\
+        annotate \\
+        $vcf \\
+        ${prefix}_annotated.vcf \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hmtnote: \$(echo \$(hmtnote --version 2>&1) | sed 's/^.*hmtnote, version //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_annotated.vcf
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hmtnote: \$(echo \$(hmtnote --version 2>&1) | sed 's/^.*hmtnote, version //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
+}

modules/hmtnote/meta.yml

@@ -0,0 +1,39 @@
+name: hmtnote
+description: Human mitochondrial variants annotation using HmtVar.
+keywords:
+  - hmtnote mitochondria annotation
+tools:
+  - hmtnote:
+      description: Human mitochondrial variants annotation using HmtVar.
+      homepage: https://github.com/robertopreste/HmtNote
+      documentation: https://hmtnote.readthedocs.io/en/latest/usage.html
+      tool_dev_url: None
+      doi: "https://doi.org/10.1101/600619"
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+  - vcf:
+      type: file
+      description: vcf file
+      pattern: "*.vcf"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - vcf:
+      type: file
+      description: annotated vcf
+      pattern: "*_annotated.vcf"
+
+authors:
+  - "@sysbiocoder"

tests/config/pytest_modules.yml

@@ -970,6 +970,10 @@ hmmer/hmmsearch:
   - modules/hmmer/hmmsearch/**
   - tests/modules/hmmer/hmmsearch/**
 
+hmtnote:
+  - modules/hmtnote/**
+  - tests/modules/hmtnote/**
+
 homer/annotatepeaks:
   - modules/homer/annotatepeaks/**
   - tests/modules/homer/annotatepeaks/**

tests/modules/hmtnote/main.nf

@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HMTNOTE } from '../../../modules/hmtnote/main.nf'
+
+workflow test_hmtnote {
+    
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+            ]
+
+    HMTNOTE ( input)
+}

tests/modules/hmtnote/nextflow.config

@@ -0,0 +1,7 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    withName: HMTNOTE {
+        ext.args = '--basic --variab'
+    }
+}

tests/modules/hmtnote/test.yml

@@ -0,0 +1,6 @@
+- name: hmtnote test_hmtnote
+  command: nextflow run ./tests/modules/hmtnote -entry test_hmtnote -c ./tests/config/nextflow.config -c ./tests/modules/hmtnote/nextflow.config
+  tags:
+    - hmtnote
+  files:
+    - path: output/hmtnote/test_annotated.vcf