From e326ecbbf6e74505eef62bea2fc0f5325144512c Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Thu, 9 Jun 2022 08:53:39 -0500
Subject: [PATCH] Add module definition for kreport2krona

---
 modules/krakentools/kreport2krona/main.nf | 36 +++++++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 modules/krakentools/kreport2krona/main.nf

diff --git a/modules/krakentools/kreport2krona/main.nf b/modules/krakentools/kreport2krona/main.nf
new file mode 100644
index 00000000..3bf46eec
--- /dev/null
+++ b/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
+    """
+}