Migrate cat/fastq to topic channel

modules/nf-core/cat/fastq/main.nf

@@ -12,7 +12,7 @@ process CAT_FASTQ {
 
     output:
     tuple val(meta), path("*.merged.fastq.gz"), emit: reads
-    path "versions.yml", emit: versions
+    tuple val("${task.process}"), val("cat"), eval("cat --version 2>&1 | head -n 1 | sed 's/^.*coreutils) //; s/ .*\$//'"), emit: versions_cat, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -24,11 +24,6 @@ process CAT_FASTQ {
         if (readList.size >= 1) {
             """
             cat ${readList.join(' ')} > ${prefix}.merged.fastq.gz
-
-            cat <<-END_VERSIONS > versions.yml
-            "${task.process}":
-                cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
-            END_VERSIONS
             """
         } else {
             error("Could not find any FASTQ files to concatenate in the process input")
@@ -42,11 +37,6 @@ process CAT_FASTQ {
             """
             cat ${read1.join(' ')} > ${prefix}_1.merged.fastq.gz
             cat ${read2.join(' ')} > ${prefix}_2.merged.fastq.gz
-
-            cat <<-END_VERSIONS > versions.yml
-            "${task.process}":
-                cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
-            END_VERSIONS
             """
         } else {
             error("Could not find any FASTQ file pairs to concatenate in the process input")
@@ -60,11 +50,6 @@ process CAT_FASTQ {
         if (readList.size >= 1) {
             """
             echo '' | gzip > ${prefix}.merged.fastq.gz
-
-            cat <<-END_VERSIONS > versions.yml
-            "${task.process}":
-                cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
-            END_VERSIONS
             """
         } else {
             error("Could not find any FASTQ files to concatenate in the process input")
@@ -75,11 +60,6 @@ process CAT_FASTQ {
             """
             echo '' | gzip > ${prefix}_1.merged.fastq.gz
             echo '' | gzip > ${prefix}_2.merged.fastq.gz
-
-            cat <<-END_VERSIONS > versions.yml
-            "${task.process}":
-                cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
-            END_VERSIONS
             """
         } else {
             error("Could not find any FASTQ file pairs to concatenate in the process input")

modules/nf-core/cat/fastq/meta.yml

@@ -34,13 +34,29 @@ output:
           description: Merged fastq file
           pattern: "*.{merged.fastq.gz}"
           ontologies: []
+  versions_cat:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - cat:
+          type: string
+          description: The tool name
+      - cat --version 2>&1 | head -n 1 | sed 's/^.*coreutils) //; s/ .*\$//':
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - cat:
+          type: string
+          description: The tool name
+      - cat --version 2>&1 | head -n 1 | sed 's/^.*coreutils) //; s/ .*\$//':
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@joseespinosa"
   - "@drpatelh"