Install KAIJU_KAIJU2KRONA

modules.json

@@ -42,6 +42,9 @@
             "kaiju/kaiju": {
                 "git_sha": "8856f127c58f6af479128be8b8df4d42e442ddbe"
             },
+            "kaiju/kaiju2krona": {
+                "git_sha": "2f0b19240430de6807b1232e6d9d0e8084e8a28f"
+            },
             "kaiju/kaiju2table": {
                 "git_sha": "538dbac98ba9c8f799536cd5a617195501439457"
             },

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