Install KRAKENTOOLS_KREPORT2KRONA module

modules.json

@@ -48,6 +48,9 @@
             "kraken2/kraken2": {
                 "git_sha": "abe025677cdd805cc93032341ab19885473c1a07"
             },
+            "krakentools/kreport2krona": {
+                "git_sha": "8b2a473f586bed003e72d2b183acc43fc0ddc422"
+            },
             "malt/run": {
                 "git_sha": "72b96f4e504eef673f2b5c13560a9d90b669129b"
             },

modules/nf-core/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/nf-core/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"