Update input in kaiju_kaiju module (#1522)

modules/kaiju/kaiju/main.nf

@@ -9,11 +9,11 @@ process KAIJU_KAIJU {
 
     input:
     tuple val(meta), path(reads)
-    tuple path(db), path(dbnodes)
+    path(db)
 
     output:
     tuple val(meta), path('*.tsv'), emit: results
-    path "versions.yml"                   , emit: versions
+    path "versions.yml"           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,11 +23,13 @@ process KAIJU_KAIJU {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def input = meta.single_end ? "-i ${reads}" : "-i ${reads[0]} -j ${reads[1]}"
     """
+    dbnodes=`find -L ${db} -name "*nodes.dmp"`
+    dbname=`find -L ${db} -name "*.fmi" -not -name "._*"`
     kaiju \\
         $args \\
         -z $task.cpus \\
-        -t ${dbnodes} \\
-        -f ${db} \\
+        -t \$dbnodes \\
+        -f \$dbname \\
         -o ${prefix}.tsv \\
         $input
 

modules/kaiju/kaiju/meta.yml

@@ -50,3 +50,4 @@ output:
 authors:
   - "@talnor"
   - "@sofstam"
+  - "@jfy133"

tests/modules/kaiju/kaiju/main.nf

@@ -2,6 +2,7 @@
 
 nextflow.enable.dsl = 2
 
+include { UNTAR       } from '../../../../modules/untar/main.nf'
 include { KAIJU_KAIJU } from '../../../../modules/kaiju/kaiju/main.nf'
 
 workflow test_kaiju_kaiju_single_end {
@@ -10,12 +11,10 @@ workflow test_kaiju_kaiju_single_end {
         [ id:'test', single_end:true ], // meta map
         file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
     ]
-    db    = [
-        file(params.test_data['sarscov2']['genome']['kaiju_fmi'], checkIfExists: true), // database
-        file(params.test_data['sarscov2']['genome']['kaiju_nodes'], checkIfExists: true) // taxon nodes
-    ]
+    db    = [ [], file(params.test_data['sarscov2']['genome']['kaiju_tar_gz'], checkIfExists: true) ]
 
-    KAIJU_KAIJU ( input, db )
+    UNTAR ( db )
+    KAIJU_KAIJU ( input, UNTAR.out.untar.map{ it[1] } )
 }
 
 workflow test_kaiju_kaiju_paired_end {
@@ -25,10 +24,9 @@ workflow test_kaiju_kaiju_paired_end {
         [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
           file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
     ]
-    db    = [
-        file(params.test_data['sarscov2']['genome']['kaiju_fmi'], checkIfExists: true), // database
-        file(params.test_data['sarscov2']['genome']['kaiju_nodes'], checkIfExists: true) // taxon nodes
-    ]
+    db    = [ [], file(params.test_data['sarscov2']['genome']['kaiju_tar_gz'], checkIfExists: true) ]
+
+    UNTAR ( db )
+    KAIJU_KAIJU ( input, UNTAR.out.untar.map{ it[1] } )
 
-    KAIJU_KAIJU ( input, db )
 }