Add haplogrep2 (#2030)

* feat added haplogrep classify

* feat made module

* fix added correct container

* feat removed md5sum

* fix trying to fix issue with version.yml

* fix some small things

* fix version

* fix on meta.yml

* fix stub run

* fix Apply suggestions from code review

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>

* fix Apply suggestions from code review2

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>

Co-authored-by: Taniguti <ltaniguti@gmail.com>
Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>

modules/haplogrep2/classify/main.nf

@@ -0,0 +1,49 @@
+process HAPLOGREP2_CLASSIFY {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::haplogrep=2.4.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/haplogrep:2.4.0--hdfd78af_0':
+        'quay.io/biocontainers/haplogrep:2.4.0--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(inputfile)
+    val(format)
+
+    output:
+    tuple val(meta), path("*.txt"), emit: txt
+    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}"
+    """
+    haplogrep \\
+        classify \\
+        $args \\
+        --in $inputfile \\
+        --out ${prefix}.txt \\
+        --format $format
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        haplogrep2: \$(echo \$(haplogrep --version 2>&1) | (sed 's/htt.*//') | (sed 's/.*v//'))
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        haplogrep2: \$(echo \$(haplogrep --version 2>&1) | (sed 's/htt.*//') | (sed 's/.*v//'))
+    END_VERSIONS
+    """
+
+}

modules/haplogrep2/classify/meta.yml

@@ -0,0 +1,43 @@
+name: "haplogrep2_classify"
+description: classification into haplogroups
+keywords:
+  - haplogroups.
+tools:
+  - "haplogrep2":
+      description: "A tool for mtDNA haplogroup classification."
+      homepage: "https://github.com/seppinho/haplogrep-cmd"
+      documentation: "https://github.com/seppinho/haplogrep-cmd"
+      tool_dev_url: "https://github.com/seppinho/haplogrep-cmd"
+      doi: ""
+      licence: "['MIT']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - inputfile:
+      type: file
+      description: valid options are hsd, vcf, or fasta files
+      pattern: "*.{vcf,vcf.gz,fasta,hsd}"
+  - format:
+      type: stringformat of file either vcf fasta or hsd
+
+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"
+  - txt:
+      type: file
+      description: text file with classification information
+      pattern: "*.{txt}"
+
+authors:
+  - "@lucpen"

tests/config/pytest_modules.yml

@@ -1139,6 +1139,10 @@ haplocheck:
   - modules/haplocheck/**
   - tests/modules/haplocheck/**
 
+haplogrep2/classify:
+  - modules/haplogrep2/classify/**
+  - tests/modules/haplogrep2/classify/**
+
 happy/happy:
   - modules/happy/happy/**
   - tests/modules/happy/happy/**

tests/modules/haplogrep2/classify/main.nf

@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HAPLOGREP2_CLASSIFY } from '../../../../modules/haplogrep2/classify/main.nf'
+
+workflow test_haplogrep2_classify {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_mito_vcf'], checkIfExists: true)
+    ]
+    format = 'vcf'
+
+    HAPLOGREP2_CLASSIFY ( input,format )
+}

tests/modules/haplogrep2/classify/nextflow.config

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

tests/modules/haplogrep2/classify/test.yml

@@ -0,0 +1,17 @@
+- name: haplogrep2 classify
+  command: nextflow run ./tests/modules/haplogrep2/classify -entry test_haplogrep2_classify -c ./tests/config/nextflow.config -c ./tests/modules/haplogrep2/classify/nextflow.config
+  tags:
+    - haplogrep2
+    - haplogrep2/classify
+  files:
+    - path: output/haplogrep2/test.txt
+    - path: output/haplogrep2/versions.yml
+
+- name: haplogrep2 classify stubs
+  command: nextflow run ./tests/modules/haplogrep2/classify -stub-run -entry test_haplogrep2_classify -c ./tests/config/nextflow.config -c ./tests/modules/haplogrep2/classify/nextflow.config
+  tags:
+    - haplogrep2
+    - haplogrep2/classify
+  files:
+    - path: output/haplogrep2/test.txt
+    - path: output/haplogrep2/versions.yml