From 8b1711d8a19696df101c73df2fa11f8994941823 Mon Sep 17 00:00:00 2001
From: Carpanzano <simone.carpanzano01@universitadipavia.it>
Date: Wed, 4 May 2022 16:38:10 +0200
Subject: [PATCH] recovering old module name

---
 modules/krona/kronadb/main.nf           | 30 +++++++++++++++++++++++++
 modules/krona/kronadb/meta.yml          | 30 +++++++++++++++++++++++++
 modules/krona/ktupdatetaxonomy/meta.yml |  2 +-
 3 files changed, 61 insertions(+), 1 deletion(-)
 create mode 100644 modules/krona/kronadb/main.nf
 create mode 100644 modules/krona/kronadb/meta.yml

diff --git a/modules/krona/kronadb/main.nf b/modules/krona/kronadb/main.nf
new file mode 100644
index 00000000..8326f219
--- /dev/null
+++ b/modules/krona/kronadb/main.nf
@@ -0,0 +1,30 @@
+def VERSION='2.7.1' // Version information not provided by tool on CLI
+
+process KRONA_KTUPDATETAXONOMY {
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::krona=2.7.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5' :
+        'quay.io/biocontainers/krona:2.7.1--pl526_5' }"
+
+    output:
+    path 'taxonomy/taxonomy.tab', emit: db
+    path "versions.yml"         , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    ktUpdateTaxonomy.sh \\
+        $args \\
+        taxonomy/
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        krona: $VERSION
+    END_VERSIONS
+    """
+}
diff --git a/modules/krona/kronadb/meta.yml b/modules/krona/kronadb/meta.yml
new file mode 100644
index 00000000..2a12aaaf
--- /dev/null
+++ b/modules/krona/kronadb/meta.yml
@@ -0,0 +1,30 @@
+name: krona_kronadb
+description: KronaTools Update Taxonomy downloads a taxonomy database
+keywords:
+  - database
+  - taxonomy
+  - krona
+tools:
+  - krona:
+      description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
+      homepage: https://github.com/marbl/Krona/wiki/KronaTools
+      documentation: https://github.com/marbl/Krona/wiki/Installing
+      tool_dev_url:
+      doi: https://doi.org/10.1186/1471-2105-12-385
+      licence:
+
+input:
+  - none: There is no input. This module downloads a pre-built taxonomy database for use with Krona Tools.
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - db:
+      type: file
+      description: A TAB separated file that contains a taxonomy database.
+      pattern: "*.{tab}"
+
+authors:
+  - "@mjakobs"
diff --git a/modules/krona/ktupdatetaxonomy/meta.yml b/modules/krona/ktupdatetaxonomy/meta.yml
index 2a12aaaf..1e0d6299 100644
--- a/modules/krona/ktupdatetaxonomy/meta.yml
+++ b/modules/krona/ktupdatetaxonomy/meta.yml
@@ -1,4 +1,4 @@
-name: krona_kronadb
+name: krona_ktupdatetaxonomy
 description: KronaTools Update Taxonomy downloads a taxonomy database
 keywords:
   - database