Update combine bracken outputs to include meta for publishing purposes

conf/modules.config

@@ -330,12 +330,12 @@ process {
         ]
     }
 
-    withName: KRAKENTOOLS_COMBINEKREPORTS {
+    withName: KRAKENTOOLS_COMBINEKREPORTS_KRAKEN {
         ext.prefix = { "kraken2_${meta.id}_combined_reports" }
         publishDir = [
             path: { "${params.outdir}/kraken2/" },
             mode: params.publish_dir_mode,
-            pattern: '*.{txt}'
+            pattern: '*.txt'
         ]
     }
 

modules.json

@@ -32,7 +32,7 @@
                     },
                     "bracken/combinebrackenoutputs": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "9c87d5fdad182590a370ea43a4ecebd200a6f6fb",
                         "installed_by": ["modules"]
                     },
                     "cat/fastq": {

modules/nf-core/bracken/combinebrackenoutputs/main.nf

@@ -1,4 +1,5 @@
 process BRACKEN_COMBINEBRACKENOUTPUTS {
+    tag "$meta.id"
     label 'process_low'
 
     conda (params.enable_conda ? "bioconda::bracken=2.7" : null)
@@ -7,10 +8,10 @@ process BRACKEN_COMBINEBRACKENOUTPUTS {
         'quay.io/biocontainers/bracken:2.7--py39hc16433a_0' }"
 
     input:
-    path input
+    tuple val(meta), path(input)
 
     output:
-    path "*.txt"       , emit: txt
+    tuple val(meta), path("*.txt"), emit: txt
     path "versions.yml"           , emit: versions
 
     when:
@@ -18,7 +19,7 @@ process BRACKEN_COMBINEBRACKENOUTPUTS {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "bracken_combined.txt"
+    def prefix = task.ext.prefix ?: "${meta.id}"
     // WARN: Version information not provided by tool on CLI.
     // Please update version string below when bumping container versions.
     def VERSION = '2.7'
@@ -26,7 +27,7 @@ process BRACKEN_COMBINEBRACKENOUTPUTS {
     combine_bracken_outputs.py \\
         $args \\
         --files ${input} \\
-        -o ${prefix}
+        -o ${prefix}.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/bracken/combinebrackenoutputs/meta.yml

@@ -12,12 +12,22 @@ tools:
       licence: ["GPL v3"]
 
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - input:
       type: file
       description: List of output files from bracken
       pattern: "*"
 
 output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - versions:
       type: file
       description: File containing software versions