Migrate drep/compare module to topic channels

modules/nf-core/drep/compare/main.nf

@@ -12,7 +12,7 @@ process DREP_COMPARE {
 
     output:
     tuple val(meta), path("${prefix}"), emit: directory
-    path "versions.yml", emit: versions
+    tuple val("${task.process}"), val("drep"), eval("dRep | head -n 2 | sed 's/.*v//g;s/ .*//g' | tail -n 1"), emit:versions_drep, topic:versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,11 +27,6 @@ process DREP_COMPARE {
         -p ${task.cpus} \\
         ${args} \\
         -g fastas/*
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        drep: \$(dRep | head -n 2 | sed 's/.*v//g;s/ .*//g' | tail -n 1)
-    END_VERSIONS
     """
 
     stub:
@@ -40,10 +35,5 @@ process DREP_COMPARE {
     """
     echo "${args}"
     mkdir -p ${prefix}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        drep: \$(dRep | head -n 2 | sed 's/.*v//g;s/ .*//g' | tail -n 1)
-    END_VERSIONS
     """
 }

modules/nf-core/drep/compare/meta.yml

@@ -1,4 +1,3 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "drep_compare"
 description: Performs rapid genome comparisons for a group of genomes and visualize
   their relatedness
@@ -13,17 +12,16 @@ keywords:
   - assembly
   - microbial genomics
   - dereplication
-
 tools:
   - "drep":
       description: "De-replication of microbial genomes assembled from multiple samples"
       homepage: "https://drep.readthedocs.io/en/latest/"
       documentation: "https://drep.readthedocs.io/en/latest/"
       tool_dev_url: "https://github.com/MrOlm/drep"
       doi: "10.1038/ismej.2017.126"
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: biotools:drep
-
 input:
   - - meta:
         type: map
@@ -35,7 +33,7 @@ input:
         description: List of FASTA files to compare
         pattern: "*.{fasta,fa,fna,fas}"
         ontologies:
-          - edam: http://edamontology.org/format_1929 # FASTA
+          - edam: http://edamontology.org/format_1929
 output:
   directory:
     - - meta:
@@ -50,13 +48,27 @@ output:
           pattern: "${prefix}/"
           ontologies:
             - edam: "http://edamontology.org/data_1049"
+  versions_drep:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - drep:
+          type: string
+          description: The name of the tool
+      - dRep | head -n 2 | sed 's/.*v//g;s/ .*//g' | tail -n 1:
+          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 name of the process
+      - drep:
+          type: string
+          description: The name of the tool
+      - dRep | head -n 2 | sed 's/.*v//g;s/ .*//g' | tail -n 1:
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@jfy133"
 maintainers:

modules/nf-core/drep/compare/tests/main.nf.test

@@ -25,8 +25,7 @@ nextflow_process {
             }
         }
 
-then {
-
+        then {
             def stablefiles = []
             file(process.out.directory.get(0).get(1)).eachFileRecurse{ file -> if (!file.isDirectory() && ["Secondary_clustering_MDS.pdf", "Secondary_clustering_dendrograms.pdf", "cluster_arguments.json", "warnings.txt", "Cdb.csv", "Ndb.csv"].find {file.toString().endsWith(it)}) {stablefiles.add(file)} }
             def unstablefiles = []
@@ -37,11 +36,10 @@ then {
                 { assert snapshot(
                     stablefiles.sort(),
                     unstablefiles.sort(),
-                    process.out.versions
-                    ).match() }
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
             )
         }
-
     }
 
     test("sarscov2 - fasta - stub") {
@@ -68,7 +66,5 @@ then {
                 { assert snapshot(process.out).match() }
             )
         }
-
     }
-
-}
+}