Fix Krona ktimporttaxonomy to allow multiple input files and simplifies database input (#1841)

* Remove quotes around input reports variable for ktImportTaxonomy as prevents supplying multiple files

* Add using prefix for output files

* Tweak meta reflecting more flexible input database specification

* Linting

* Fix finding the correct directory

* Update main.nf

* Fix database inport

* Prettier

modules/krona/ktimporttaxonomy/main.nf

@@ -10,7 +10,7 @@ process KRONA_KTIMPORTTAXONOMY {
 
     input:
     tuple val(meta), path(report)
-    path  "taxonomy/taxonomy.tab"
+    path taxonomy, stageAs: 'taxonomy.tab'
 
     output:
     tuple val(meta), path ('*.html'), emit: html
@@ -21,12 +21,17 @@ process KRONA_KTIMPORTTAXONOMY {
 
     script:
     def args = task.ext.args ?: ''
+    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 \\
         $args \\
-        -tax taxonomy/ \\
-        "$report"
+        -o ${prefix}.html \\
+        -tax \$TAXONOMY/ \\
+        $report
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

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."

tests/modules/krona/ktimporttaxonomy/test.yml

@@ -1,23 +1,17 @@
 - name: krona ktimporttaxonomy test_krona_ktimporttaxonomy_reads
-  command: nextflow run tests/modules/krona/ktimporttaxonomy -entry test_krona_ktimporttaxonomy_reads -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/krona/ktimporttaxonomy -entry test_krona_ktimporttaxonomy_reads -c ./tests/config/nextflow.config  -c ./tests/modules/krona/ktimporttaxonomy/nextflow.config
   tags:
-    - krona
     - krona/ktimporttaxonomy
+    - krona
   files:
-    - path: output/krona/taxonomy.krona.html
-      contains:
-        - "DOCTYPE html PUBLIC"
-    - path: output/krona/versions.yml
-      md5sum: 660a8c151191bf4c63bd96db2c7fe503
+    - path: output/krona/test.html
+      contains: ["Krona is a flexible tool for exploring the relative proportions of"]
 
 - name: krona ktimporttaxonomy test_krona_ktimporttaxonomy_report
-  command: nextflow run tests/modules/krona/ktimporttaxonomy -entry test_krona_ktimporttaxonomy_report -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/krona/ktimporttaxonomy -entry test_krona_ktimporttaxonomy_report -c ./tests/config/nextflow.config  -c ./tests/modules/krona/ktimporttaxonomy/nextflow.config
   tags:
-    - krona
     - krona/ktimporttaxonomy
+    - krona
   files:
-    - path: output/krona/taxonomy.krona.html
-      contains:
-        - "DOCTYPE html PUBLIC"
-    - path: output/krona/versions.yml
-      md5sum: 8a593c16bb2d4132638fb0fc342fe2b7
+    - path: output/krona/test.html
+      contains: ["Krona is a flexible tool for exploring the relative proportions of"]