Add MEGAN/RMA2INFO (#1513)

* fix: remove left-over unnecessary code

* Add megan/rma2info

* Attempt at fixing test

* Right yml formatting

* Get the versios reporting correct

modules/megan/rma2info/main.nf

@@ -0,0 +1,38 @@
+process MEGAN_RMA2INFO {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::megan=6.21.7" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/megan:6.21.7--h9ee0642_0':
+        'quay.io/biocontainers/megan:6.21.7--h9ee0642_0' }"
+
+    input:
+    tuple val(meta), path(rma6)
+    val(megan_summary)
+
+    output:
+    tuple val(meta), path("*.txt.gz")               , emit: txt
+    tuple val(meta), path("*.megan"), optional: true, emit: megan_summary
+    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 summary = megan_summary ? "-es ${prefix}.megan" : ""
+    """
+    rma2info \\
+        -i ${rma6} \\
+        -o ${prefix}.txt.gz \\
+        ${summary} \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        megan: \$(echo \$(rma2info 2>&1) | grep version | sed 's/.*version //g;s/, built.*//g')
+    END_VERSIONS
+    """
+}

modules/megan/rma2info/meta.yml

@@ -0,0 +1,51 @@
+name: "megan_rma2info"
+description: Analyses an RMA file and exports information in text format
+keywords:
+  - megan
+  - rma6
+  - classification
+  - conversion
+tools:
+  - "megan":
+      description: "A tool for studying the taxonomic content of a set of DNA reads"
+      homepage: "https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/megan6/"
+      documentation: "https://software-ab.informatik.uni-tuebingen.de/download/megan6/welcome.html"
+      tool_dev_url: "https://github.com/husonlab/megan-ce"
+      doi: "10.1371/journal.pcbi.1004957"
+      licence: "['GPL >=3']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - rma6:
+      type: file
+      description: RMA6 file from MEGAN or MALT
+      pattern: "*.rma6"
+  - megan_summary:
+      type: boolean
+      description: Specify whether to generate an MEGAN summary file
+
+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: Compressed text file
+      pattern: "*.txt.gz"
+  - megan_summary:
+      type: file
+      description: Optionally generated MEGAN summary file
+      pattern: "*.megan"
+
+authors:
+  - "@jfy133"

tests/config/pytest_modules.yml

@@ -1138,6 +1138,10 @@ megahit:
   - modules/megahit/**
   - tests/modules/megahit/**
 
+megan/rma2info:
+  - modules/megan/rma2info/**
+  - tests/modules/megan/rma2info/**
+
 meningotype:
   - modules/meningotype/**
   - tests/modules/meningotype/**

tests/modules/megan/rma2info/main.nf

@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MEGAN_RMA2INFO } from '../../../../modules/megan/rma2info/main.nf'
+
+workflow test_megan_rma2info {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file('https://github.com/nf-core/test-datasets/raw/a7e61654553887475a2f7178108587ecd9b54608/data/delete_me/malt/test.rma6', checkIfExists: true)
+    ]
+    megan_summary = true
+
+    MEGAN_RMA2INFO ( input, megan_summary )
+}

tests/modules/megan/rma2info/nextflow.config

@@ -0,0 +1,9 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: MEGAN_RMA2INFO {
+        ext.args = "-c2c Taxonomy"
+    }
+
+}

tests/modules/megan/rma2info/test.yml

@@ -0,0 +1,12 @@
+- name: megan rma2info test_megan_rma2info
+  command: nextflow run tests/modules/megan/rma2info -entry test_megan_rma2info -c tests/config/nextflow.config
+  tags:
+    - megan
+    - megan/rma2info
+  files:
+    - path: output/megan/test.megan
+      contains:
+        - "@Creator"
+    - path: output/megan/test.txt.gz
+      md5sum: 5c3b876aa0abef12158bcd7c3702740f
+    - path: output/megan/versions.yml