Get fixed Krona module and add Krona taxonomy to test profile

conf/test.config

@@ -38,6 +38,7 @@ params {
     run_centrifuge                        = true
     run_diamond                           = true
     run_krona                             = true
+    krona_taxonomy_directory              = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
     malt_save_reads                       = true
     kraken2_save_reads                    = true
     centrifuge_save_reads                 = true

modules.json

@@ -58,7 +58,7 @@
                 "git_sha": "8b2a473f586bed003e72d2b183acc43fc0ddc422"
             },
             "krona/ktimporttaxonomy": {
-                "git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
+                "git_sha": "0e9fd9370ad1845870b8a9c63fcc47d999a1739e"
             },
             "krona/ktimporttext": {
                 "git_sha": "cdefbec66999c0b49d8bfeea9d6f9d19056635a2"

modules/nf-core/modules/krona/ktimporttaxonomy/main.nf

@@ -10,7 +10,7 @@ process KRONA_KTIMPORTTAXONOMY {
 
     input:
     tuple val(meta), path(report)
-    path taxonomy
+    path taxonomy, stageAs: 'taxonomy.tab'
 
     output:
     tuple val(meta), path ('*.html'), emit: html
@@ -24,10 +24,13 @@ process KRONA_KTIMPORTTAXONOMY {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = '2.8' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
+    TAXONOMY=\$(find -L . -name '*.tab' -exec dirname {} \\;)
+    echo \$TAXONOMY
+
     ktImportTaxonomy \\
         $args \\
         -o ${prefix}.html \\
-        -tax $taxonomy \\
+        -tax \$TAXONOMY/ \\
         $report
 
     cat <<-END_VERSIONS > versions.yml
@@ -35,4 +38,4 @@ process KRONA_KTIMPORTTAXONOMY {
         krona: $VERSION
     END_VERSIONS
     """
-}
+}

modules/nf-core/modules/krona/ktimporttaxonomy/meta.yml

@@ -25,9 +25,10 @@ input:
   - database:
       type: file
       description: |
-        Path to the taxonomy database .tab file downloaded by krona/ktUpdateTaxonomy
-        The file will be saved under a folder named "taxonomy" as "taxonomy/taxonomy.tab".
-        The parent folder will be passed as argument to ktImportTaxonomy.
+        Path to a Krona taxonomy .tab file normally downloaded and generated by
+        krona/ktUpdateTaxonomy. Custom taxonomy files can have any name, but
+        must end in `.tab`.
+      pattern: "*tab"
   - report:
       type: file
       description: "A tab-delimited file with taxonomy IDs and (optionally) query IDs, magnitudes, and scores.  Query IDs are taken from column 1, taxonomy IDs from column 2, and scores from column 3.  Lines beginning with # will be ignored."