New module: krakentools/kreport2krona (#1746)

* Add module definition for kreport2krona

* Add metadata for kreport2krona module

* Add tests for kreport2krona

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

modules/krakentools/kreport2krona/main.nf

@@ -0,0 +1,36 @@
+def VERSION = '1.2' // Version information not provided by tool on CLI
+
+process KRAKENTOOLS_KREPORT2KRONA {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::krakentools=1.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0':
+        'quay.io/biocontainers/krakentools:1.2--pyh5e36f6f_0' }"
+
+    input:
+    tuple val(meta), path(kreport)
+
+    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}"
+    """
+    kreport2krona.py \\
+        -r ${kreport} \\
+        -o ${prefix}.txt \\
+        ${args}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        kreport2krona.py: ${VERSION}
+    END_VERSIONS
+    """
+}

modules/krakentools/kreport2krona/meta.yml

@@ -0,0 +1,41 @@
+name: krakentools_kreport2krona
+description: Takes a Kraken report file and prints out a krona-compatible TEXT file
+keywords:
+  - kraken
+  - krona
+  - metagenomics
+  - visualization
+tools:
+  - krakentools:
+      description: KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.
+      homepage: https://github.com/jenniferlu717/KrakenTools
+      licence: ["GPL v3"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - kreport:
+      type: file
+      description: Kraken report
+      pattern: "*.{txt,kreport}"
+
+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"
+  - krona:
+      type: file
+      description: Krona text-based input file converted from Kraken report
+      pattern: "*.{txt,krona}"
+
+authors:
+  - "@MillironX"

tests/config/pytest_modules.yml

@@ -1146,6 +1146,10 @@ kraken2/kraken2:
   - modules/untar/**
   - tests/modules/kraken2/kraken2/**
 
+krakentools/kreport2krona:
+  - modules/krakentools/kreport2krona/**
+  - tests/modules/krakentools/kreport2krona/**
+
 krona/kronadb:
   - modules/krona/kronadb/**
   - tests/modules/krona/kronadb/**

tests/modules/krakentools/kreport2krona/main.nf

@@ -0,0 +1,20 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR } from '../../../../modules/untar/main'
+include { KRAKEN2_KRAKEN2 } from '../../../../modules/kraken2/kraken2/main'
+include { KRAKENTOOLS_KREPORT2KRONA } from '../../../../modules/krakentools/kreport2krona/main'
+
+workflow test_krakentools_kreport2krona {
+
+    input = Channel.of([ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ])
+    db    = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ]
+
+    UNTAR ( db )
+    KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] }, false, false )
+    KRAKENTOOLS_KREPORT2KRONA ( KRAKEN2_KRAKEN2.out.report )
+}

tests/modules/krakentools/kreport2krona/nextflow.config

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

tests/modules/krakentools/kreport2krona/test.yml

@@ -0,0 +1,8 @@
+- name: krakentools kreport2krona test_krakentools_kreport2krona
+  command: nextflow run ./tests/modules/krakentools/kreport2krona -entry test_krakentools_kreport2krona -c ./tests/config/nextflow.config  -c ./tests/modules/krakentools/kreport2krona/nextflow.config
+  tags:
+    - krakentools/kreport2krona
+    - krakentools
+  files:
+    - path: output/krakentools/test.txt
+      md5sum: c89a9db7acbdba9dea0fe246bcaa85c1