chore(modules): migrate adapterremoval & adapterremovalfixprefix to new version output format

modules/nf-core/adapterremoval/main.nf

@@ -19,7 +19,7 @@ process ADAPTERREMOVAL {
     tuple val(meta), path("${prefix}.collapsed.truncated.fastq.gz"), emit: collapsed_truncated, optional: true
     tuple val(meta), path("${prefix}.paired.fastq.gz")             , emit: paired_interleaved , optional: true
     tuple val(meta), path('*.settings')                            , emit: settings
-    path "versions.yml"                                            , emit: versions
+    tuple val("${task.process}"), val('adapterremoval'), eval('AdapterRemoval --version 2>&1 | sed -e "s/.* //g"'), emit: versions_adapterremoval, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -50,10 +50,7 @@ process ADAPTERREMOVAL {
         ensure_fastq '${prefix}.truncated.gz'
         ensure_fastq '${prefix}.discarded.gz'
 
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
-        END_VERSIONS
+
         """
     } else {
         """
@@ -82,10 +79,7 @@ process ADAPTERREMOVAL {
         ensure_fastq '${prefix}.collapsed.truncated.gz'
         ensure_fastq '${prefix}.paired.gz'
 
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
-        END_VERSIONS
+
         """
     }
 
@@ -110,9 +104,6 @@ process ADAPTERREMOVAL {
         fi
     fi
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
-    END_VERSIONS
+
     """
 }

modules/nf-core/adapterremoval/meta.yml

@@ -122,13 +122,27 @@ output:
           pattern: "*.settings"
           ontologies:
             - edam: "http://edamontology.org/format_2330" # Textual format
+  versions_adapterremoval:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - adapterremoval:
+          type: string
+          description: The tool name
+      - AdapterRemoval --version 2>&1 | sed "s/ ver. //g":
+          type: eval
+          description: The expression to obtain the version of adapterremoval
+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
+      - adapterremoval:
+          type: string
+          description: The tool name
+      - AdapterRemoval --version 2>&1 | sed "s/.* //g":
+          type: eval
+          description: The expression to obtain the version of adapterremoval
 authors:
   - "@maxibor"
   - "@jfy133"

modules/nf-core/adapterremoval/tests/main.nf.test

@@ -29,9 +29,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.singles_truncated,
-                    process.out.settings,
-                    process.out.versions
+                    process.out
                 ).match() },
             )
         }
@@ -61,9 +59,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.paired_truncated,
-                    process.out.settings,
-                    process.out.versions
+                    process.out
                 ).match() }
             )
         }
@@ -92,11 +88,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.paired_truncated,
-                    process.out.collapsed,
-                    file(process.out.collapsed_truncated[0][1]).name, // Check for present but is empty
-                    process.out.settings,
-                    process.out.versions
+                    process.out
                 ).match() }
             )
         }
@@ -126,9 +118,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.paired_truncated,
-                    process.out.settings,
-                    process.out.versions
+                    process.out
                 ).match() }
             )
         }
@@ -158,8 +148,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out,
-                    path(process.out.versions[0]).yaml
+                    process.out
                 ).match() }
             )
         }
@@ -186,8 +175,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out,
-                    path(process.out.versions[0]).yaml
+                    process.out
                 ).match() }
             )
         }
@@ -217,8 +205,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out,
-                    path(process.out.versions[0]).yaml
+                    process.out
                 ).match() }
             )
         }