Add KAIJU2KRONA module (#1800)

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

modules/kaiju/kaiju2krona/main.nf

@@ -0,0 +1,39 @@
+process KAIJU_KAIJU2KRONA {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
+        'quay.io/biocontainers/kaiju:1.8.2--h5b5514e_1' }"
+
+    input:
+    tuple val(meta), path(tsv)
+    path(db)
+
+    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}"
+    """
+    dbnodes=`find -L ${db} -name "*nodes.dmp"`
+    dbnames=`find -L ${db} -name "*names.dmp"`
+    kaiju2krona \\
+        $args \\
+        -t \$dbnodes \\
+        -n \$dbnames \\
+        -i ${tsv} \\
+        -o ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
+    END_VERSIONS
+    """
+}

modules/kaiju/kaiju2krona/meta.yml

@@ -0,0 +1,44 @@
+name: kaiju_kaiju2krona
+description: Convert Kaiju's tab-separated output file into a tab-separated text file which can be imported into Krona.
+keywords:
+  - taxonomy
+  - visualisation
+  - krona chart
+  - metagenomics
+tools:
+  - "kaiju":
+      description: Fast and sensitive taxonomic classification for metagenomics
+      homepage: https://kaiju.binf.ku.dk/
+      documentation: https://github.com/bioinformatics-centre/kaiju/blob/master/README.md
+      tool_dev_url: https://github.com/bioinformatics-centre/kaiju
+      doi: "10.1038/ncomms11257"
+      licence: ["GNU GPL v3"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - tsv:
+      type: file
+      description: Kaiju tab-separated output file
+      pattern: "*.{tsv,txt}"
+
+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: Krona text-based input file converted from Kaiju report
+      pattern: "*.{txt,krona}"
+
+authors:
+  - "@MillironX"

tests/config/pytest_modules.yml

@@ -1137,6 +1137,10 @@ kaiju/kaiju:
   - modules/kaiju/kaiju/**
   - tests/modules/kaiju/kaiju/**
 
+kaiju/kaiju2krona:
+  - modules/kaiju/kaiju2krona/**
+  - tests/modules/kaiju/kaiju2krona/**
+
 kaiju/kaiju2table:
   - modules/kaiju/kaiju2table/**
   - tests/modules/kaiju/kaiju2table/**

tests/modules/kaiju/kaiju2krona/main.nf

@@ -0,0 +1,20 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR } from '../../../../modules/untar/main.nf'
+include { KAIJU_KAIJU } from '../../../../modules/kaiju/kaiju/main.nf'
+include { KAIJU_KAIJU2KRONA } from '../../../../modules/kaiju/kaiju2krona/main.nf'
+
+workflow test_kaiju_kaiju2krona {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+    db = [ [], file(params.test_data['sarscov2']['genome']['kaiju_tar_gz'], checkIfExists: true) ]
+
+    UNTAR ( db )
+    KAIJU_KAIJU ( input, UNTAR.out.untar.map{ it[1] } )
+    KAIJU_KAIJU2KRONA ( KAIJU_KAIJU.out.results , UNTAR.out.untar.map{ it[1] } )
+}

tests/modules/kaiju/kaiju2krona/nextflow.config

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

tests/modules/kaiju/kaiju2krona/test.yml

@@ -0,0 +1,8 @@
+- name: kaiju kaiju2krona test_kaiju_kaiju2krona
+  command: nextflow run ./tests/modules/kaiju/kaiju2krona -entry test_kaiju_kaiju2krona -c ./tests/config/nextflow.config  -c ./tests/modules/kaiju/kaiju2krona/nextflow.config
+  tags:
+    - kaiju/kaiju2krona
+    - kaiju
+  files:
+    - path: output/kaiju/test.txt
+      md5sum: 68b2309d37767e444193fa6cea7c0494