Update KRAKENTOOLS/COMBINEKREPORTS (#2043)

* Update main.nf

* Update meta.yml

* Re-add logos as not staged in a way that works with MultiQC config files

* Add meta to combinekreports

modules/krakentools/combinekreports/main.nf

@@ -7,10 +7,10 @@ process KRAKENTOOLS_COMBINEKREPORTS {
         'quay.io/biocontainers/krakentools:1.2--pyh5e36f6f_0' }"
 
     input:
-    path kreports
+    tuple val(meta), path(kreports)
 
     output:
-    path "*.txt", emit: txt
+    tuple val(meta), path("*.txt"), emit: txt
     path "versions.yml", emit: versions
 
     when:
@@ -18,12 +18,12 @@ process KRAKENTOOLS_COMBINEKREPORTS {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "kreports_combined.txt"
+    prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = '1.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     combine_kreports.py \\
         -r ${kreports} \\
-        -o ${prefix} \\
+        -o ${prefix}.txt \\
         ${args}
 
     cat <<-END_VERSIONS > versions.yml

modules/krakentools/combinekreports/meta.yml

@@ -14,12 +14,22 @@ tools:
       licence: ["GPL v3"]
 
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - kreports:
       type: file
       description: List of kraken-style report files
       pattern: "*.{txt,kreport}"
 
 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

tests/modules/krakentools/combinekreports/main.nf

@@ -19,5 +19,5 @@ workflow test_krakentools_combinekreports {
     UNTAR ( db )
     KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] }, false, false )
 
-    KRAKENTOOLS_COMBINEKREPORTS ( KRAKEN2_KRAKEN2.out.report.map{ [ it[1] ] }.collect().dump() )
+    KRAKENTOOLS_COMBINEKREPORTS ( KRAKEN2_KRAKEN2.out.report.map{ [[id:"test"], it[1]] }.groupTuple().dump())
 }

tests/modules/krakentools/combinekreports/test.yml

@@ -1,9 +1,9 @@
 - name: krakentools combinekreports test_krakentools_combinekreports
   command: nextflow run ./tests/modules/krakentools/combinekreports -entry test_krakentools_combinekreports -c ./tests/config/nextflow.config  -c ./tests/modules/krakentools/combinekreports/nextflow.config
   tags:
-    - krakentools/combinekreports
     - krakentools
+    - krakentools/combinekreports
   files:
-    - path: output/krakentools/kreports_combined.txt
+    - path: output/krakentools/test.txt
       contains:
         - "#Number of Samples: 2"