Improves kraken2 output glob (#1987)

* Improves kraken2 output glob

* Further strictness

* Further improvements

modules/kraken2/kraken2/main.nf

@@ -14,11 +14,11 @@ process KRAKEN2_KRAKEN2 {
     val save_reads_assignment
 
     output:
-    tuple val(meta), path('*classified*')     , optional:true, emit: classified_reads_fastq
-    tuple val(meta), path('*unclassified*')   , optional:true, emit: unclassified_reads_fastq
-    tuple val(meta), path('*classifiedreads*'), optional:true, emit: classified_reads_assignment
-    tuple val(meta), path('*report.txt')                     , emit: report
-    path "versions.yml"                                      , emit: versions
+    tuple val(meta), path('*.classified{.,_}*')     , optional:true, emit: classified_reads_fastq
+    tuple val(meta), path('*.unclassified{.,_}*')   , optional:true, emit: unclassified_reads_fastq
+    tuple val(meta), path('*classifiedreads.txt')   , optional:true, emit: classified_reads_assignment
+    tuple val(meta), path('*report.txt')                           , emit: report
+    path "versions.yml"                                            , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -29,9 +29,9 @@ process KRAKEN2_KRAKEN2 {
     def paired       = meta.single_end ? "" : "--paired"
     def classified   = meta.single_end ? "${prefix}.classified.fastq"   : "${prefix}.classified#.fastq"
     def unclassified = meta.single_end ? "${prefix}.unclassified.fastq" : "${prefix}.unclassified#.fastq"
-    def classified_command = save_output_fastqs ? "--classified-out ${classified}" : ""
-    def unclassified_command = save_output_fastqs ? "--unclassified-out ${unclassified}" : ""
-    def readclassification_command = save_reads_assignment ? "--output ${prefix}.kraken2.classifiedreads.txt" : ""
+    def classified_option = save_output_fastqs ? "--classified-out ${classified}" : ""
+    def unclassified_option = save_output_fastqs ? "--unclassified-out ${unclassified}" : ""
+    def readclassification_option = save_reads_assignment ? "--output ${prefix}.kraken2.classifiedreads.txt" : ""
     def compress_reads_command = save_output_fastqs ? "pigz -p $task.cpus *.fastq" : ""
 
     """
@@ -40,9 +40,9 @@ process KRAKEN2_KRAKEN2 {
         --threads $task.cpus \\
         --report ${prefix}.kraken2.report.txt \\
         --gzip-compressed \\
-        $unclassified_command \\
-        $classified_command \\
-        $readclassification_command \\
+        $unclassified_option \\
+        $classified_option \\
+        $readclassification_option \\
         $paired \\
         $args \\
         $reads