fixing suggestions from PR

modules/krona/ktimporttaxonomy/main.nf

@@ -24,9 +24,9 @@ process KRONA_KTIMPORTTAXONOMY {
     def args = task.ext.args ?: ''
     """
     ktImportTaxonomy \\
-        "$report" \\
         $args \\
-        -tax taxonomy
+        -tax taxonomy/ \\
+        "$report"
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/krona/ktupdatetaxonomy/main.nf

@@ -1,6 +1,6 @@
 def VERSION='2.7.1' // Version information not provided by tool on CLI
 
-process KRONA_KRONADB {
+process KRONA_KTUPDATETAXONOMY {
     label 'process_low'
 
     conda (params.enable_conda ? "bioconda::krona=2.7.1" : null)
@@ -20,7 +20,7 @@ process KRONA_KRONADB {
     """
     ktUpdateTaxonomy.sh \\
         $args \\
-        taxonomy
+        taxonomy/
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

tests/config/pytest_modules.yml

@@ -1046,9 +1046,9 @@ kraken2/kraken2:
   - modules/untar/**
   - tests/modules/kraken2/kraken2/**
 
-krona/kronadb:
-  - modules/krona/kronadb/**
-  - tests/modules/krona/kronadb/**
+krona/ktupdatetaxonomy:
+  - modules/krona/ktupdatetaxonomy/**
+  - tests/modules/krona/ktupdatetaxonomy/**
 
 krona/ktimporttaxonomy:
   - modules/krona/ktimporttaxonomy/**

tests/config/test_data.config

@@ -113,6 +113,7 @@ params {
             'metagenome' {
                 classified_reads_assignment                    = "${test_data_dir}/genomics/sarscov2/metagenome/test_1.kraken2.reads.txt"
                 kraken_report                                  = "${test_data_dir}/genomics/sarscov2/metagenome/test_1.kraken2.report.txt"
+                krona_taxonomy                                 = "${test_data_dir}/genomics/sarscov2/metagenome/krona_taxonomy.tab"
             }
         }
         'homo_sapiens' {

tests/modules/krona/kronadb/main.nf

@@ -1,9 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { KRONA_KRONADB } from '../../../../modules/krona/kronadb/main.nf'
-
-workflow test_krona_kronadb {
-    KRONA_KRONADB ( )
-}

tests/modules/krona/kronadb/test.yml

@@ -1,7 +0,0 @@
-- name: krona kronadb test_krona_kronadb
-  command: nextflow run ./tests/modules/krona/kronadb -entry test_krona_kronadb -c ./tests/config/nextflow.config -c ./tests/modules/krona/kronadb/nextflow.config
-  tags:
-    - krona
-    - krona/kronadb
-  files:
-    - path: output/krona/taxonomy/taxonomy.tab

tests/modules/krona/ktimporttaxonomy/main.nf

@@ -2,8 +2,8 @@
 
 nextflow.enable.dsl = 2
 
-include { KRONA_KTIMPORTTAXONOMY as KRONA_TAXONOMY_READS  } from '../../../../modules/krona/ktimporttaxonomy/main.nf'
-include { KRONA_KTIMPORTTAXONOMY as KRONA_TAXONOMY_REPORT } from '../../../../modules/krona/ktimporttaxonomy/main.nf'
+include { KRONA_KTIMPORTTAXONOMY as KRONA_KTIMPORTTAXONOMY_READS  } from '../../../../modules/krona/ktimporttaxonomy/main.nf'
+include { KRONA_KTIMPORTTAXONOMY as KRONA_KTIMPORTTAXONOMY_REPORT } from '../../../../modules/krona/ktimporttaxonomy/main.nf'
 
 workflow test_krona_ktimporttaxonomy_reads {
 
@@ -11,9 +11,9 @@ workflow test_krona_ktimporttaxonomy_reads {
         [ id:'test', single_end:false ], // meta map
         file(params.test_data['sarscov2']['metagenome']['classified_reads_assignment'], checkIfExists: true)
     ]
-    taxonomy = file("https://raw.githubusercontent.com/lescai/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab")
+    taxonomy = file(params.test_data['sarscov2']['metagenome']['krona_taxonomy'], checkIfExists: true)
 
-    KRONA_TAXONOMY_READS ( input, taxonomy )
+    KRONA_KTIMPORTTAXONOMY_READS ( input, taxonomy )
 }
 
 workflow test_krona_ktimporttaxonomy_report {
@@ -22,7 +22,7 @@ workflow test_krona_ktimporttaxonomy_report {
         [ id:'test', single_end:false ], // meta map
         file(params.test_data['sarscov2']['metagenome']['kraken_report'], checkIfExists: true)
     ]
-    taxonomy = file("https://raw.githubusercontent.com/lescai/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab")
+    taxonomy = file(params.test_data['sarscov2']['metagenome']['krona_taxonomy'], checkIfExists: true)
 
-    KRONA_TAXONOMY_REPORT ( input, taxonomy )
+    KRONA_KTIMPORTTAXONOMY_REPORT ( input, taxonomy )
 }

tests/modules/krona/ktupdatetaxonomy/main.nf

@@ -0,0 +1,9 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { KRONA_KTUPDATETAXONOMY } from '../../../../modules/krona/ktupdatetaxonomy/main.nf'
+
+workflow test_krona_ktupdatetaxonomy {
+    KRONA_KTUPDATETAXONOMY ( )
+}

tests/modules/krona/ktupdatetaxonomy/test.yml

@@ -0,0 +1,7 @@
+- name: krona ktupdatetaxonomy test_krona_ktupdatetaxonomy
+  command: nextflow run ./tests/modules/krona/ktupdatetaxonomy -entry test_krona_ktupdatetaxonomy -c ./tests/config/nextflow.config -c ./tests/modules/krona/ktupdatetaxonomy/nextflow.config
+  tags:
+    - krona
+    - krona/ktupdatetaxonomy
+  files:
+    - path: output/krona/taxonomy/taxonomy.tab