Adds version topic channel to SAMTOOLS_STATS

Author: mribeirodantas

modules/nf-core/samtools/stats/main.nf

@@ -13,8 +13,8 @@ process SAMTOOLS_STATS {
 
     output:
     tuple val(meta), path("*.stats"), emit: stats
-    path  "versions.yml"            , emit: versions
-
+    tuple val("${task.process}"), val('samtools'), eval('samtools --version | head -1 | sed -e "s/samtools //"'), emit: versions_samtools, topic: versions
+    
     when:
     task.ext.when == null || task.ext.when
 
@@ -28,21 +28,11 @@ process SAMTOOLS_STATS {
         ${reference} \\
         ${input} \\
         > ${prefix}.stats
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.stats
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 }

modules/nf-core/samtools/stats/meta.yml

@@ -55,13 +55,28 @@ output:
           description: File containing samtools stats output
           pattern: "*.{stats}"
           ontologies: []
-  versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+  versions_samtools:
+    - - ${task.process}:
+          type: string
+          description: Name of the process
+      - samtools:
+          type: string
+          description: Name of the tool
+      - samtools --version | head -1 | sed -e "s/samtools //:
+          type: string
+          description: Version of samtools used
+
+topics:
+  - versions:
+      - - process:
+            type: string
+            description: The process the versions were collected from
+        - tool:
+            type: string
+            description: The tool name
+        - version:
+            type: string
+            description: The version of the tool
 authors:
   - "@drpatelh"
   - "@FriederikeHanssen"