Swap verifybamid to topic

modules/nf-core/verifybamid/verifybamid/main.nf

@@ -2,6 +2,7 @@ process VERIFYBAMID_VERIFYBAMID {
     tag "${meta.id}"
     label "process_single"
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/verifybamid%3A1.1.3--h5b5514e_6':
@@ -12,21 +13,22 @@ process VERIFYBAMID_VERIFYBAMID {
     path refvcf
 
     output:
-    tuple val(meta), path("*.log")                                  , emit: log
-    tuple val(meta), path("*.selfSM")                , optional:true, emit: selfsm
-    tuple val(meta), path("*.depthSM")               , optional:true, emit: depthsm
-    tuple val(meta), path("*.selfRG")                , optional:true, emit: selfrg
-    tuple val(meta), path("*.depthRG")               , optional:true, emit: depthrg
-    tuple val(meta), path("*.bestSM")                , optional:true, emit: bestsm
-    tuple val(meta), path("*.bestRG")                , optional:true, emit: bestrg
-    path "versions.yml"                                             , emit: versions
+    tuple val(meta), path("*.log")    , emit: log
+    tuple val(meta), path("*.selfSM") , emit: selfsm , optional:true
+    tuple val(meta), path("*.depthSM"), emit: depthsm, optional:true
+    tuple val(meta), path("*.selfRG") , emit: selfrg , optional:true
+    tuple val(meta), path("*.depthRG"), emit: depthrg, optional:true
+    tuple val(meta), path("*.bestSM") , emit: bestsm , optional:true
+    tuple val(meta), path("*.bestRG") , emit: bestrg , optional:true
+    tuple val("${task.process}"), val('verifybamid'), eval("echo '1.1.3'"), emit: versions_verifybamid, topic: versions
+    // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
+    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '1.1.3' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
     """
     verifyBamID \\
@@ -35,10 +37,16 @@ process VERIFYBAMID_VERIFYBAMID {
         --out ${prefix} \\
         ${args} \\
         > ${prefix}.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        verifybamid: $VERSION
-    END_VERSIONS
+    """
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.log
+    touch ${prefix}.bestSM
+    touch ${prefix}.bestRG
+    touch ${prefix}.depthRG
+    touch ${prefix}.depthSM
+    touch ${prefix}.selfRG
+    touch ${prefix}.selfSM
     """
 }

modules/nf-core/verifybamid/verifybamid/meta.yml

@@ -1,7 +1,7 @@
 name: "verifybamid_verifybamid"
-description: Detecting and estimating inter-sample DNA contamination became a crucial
-  quality assessment step to ensure high quality sequence reads and reliable downstream
-  analysis.
+description: Detecting and estimating inter-sample DNA contamination became a
+  crucial quality assessment step to ensure high quality sequence reads and
+  reliable downstream analysis.
 keywords:
   - qc
   - contamination
@@ -15,7 +15,8 @@ tools:
       documentation: "http://genome.sph.umich.edu/wiki/VerifyBamID"
       tool_dev_url: "https://github.com/statgen/verifyBamID"
       doi: "10.1016/j.ajhg.2012.09.004"
-      licence: ["GPL v3"]
+      licence:
+        - "GPL v3"
       identifier: biotools:verifybamid
 input:
   - - meta:
@@ -64,8 +65,8 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "*.selfSM":
           type: file
-          description: Per-sample statistics describing how well the sample matches
-            to the annotated sample.
+          description: Per-sample statistics describing how well the sample
+            matches to the annotated sample.
           pattern: "*.selfSM"
           ontologies: []
   depthsm:
@@ -87,8 +88,9 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "*.selfRG":
           type: file
-          description: Per-readGroup statistics describing how well each lane matches
-            to the annotated sample. (available only without --ignoreRG option)
+          description: Per-readGroup statistics describing how well each lane
+            matches to the annotated sample. (available only without --ignoreRG
+            option)
           pattern: "*.selfRG"
           ontologies: []
   depthrg:
@@ -99,8 +101,8 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "*.depthRG":
           type: file
-          description: The depth distribution of the sequence reads per readGroup. (available
-            only without --ignoreRG option)
+          description: The depth distribution of the sequence reads per readGroup.
+            (available only without --ignoreRG option)
           pattern: "*.depthRG"
           ontologies: []
   bestsm:
@@ -111,8 +113,8 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "*.bestSM":
           type: file
-          description: Per-sample best-match statistics with best-matching sample among
-            the genotyped sample (available only with --best option)
+          description: Per-sample best-match statistics with best-matching sample
+            among the genotyped sample (available only with --best option)
           pattern: "*.bestSM"
           ontologies: []
   bestrg:
@@ -123,18 +125,34 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "*.bestRG":
           type: file
-          description: Per-readgroup best-match statistics with best-matching sample
-            among the genotyped sample (available only with --best and without --ignoreRG
-            option)
+          description: Per-readgroup best-match statistics with best-matching
+            sample among the genotyped sample (available only with --best and
+            without --ignoreRG option)
           pattern: "*.bestRG"
           ontologies: []
+  versions_verifybamid:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - verifybamid:
+          type: string
+          description: The name of the tool
+      - echo '1.1.3':
+          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
+      - verifybamid:
+          type: string
+          description: The name of the tool
+      - echo '1.1.3':
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@manifestoso"
 maintainers:

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

@@ -4,7 +4,6 @@ nextflow_process {
     name "Test Process VERIFYBAMID_VERIFYBAMID"
     script "../main.nf"
     process "VERIFYBAMID_VERIFYBAMID"
-    config "./nextflow.config"
 
     tag "modules"
     tag "modules_nfcore"
@@ -27,18 +26,35 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    file(process.out.log[0][1]).name,
-                    process.out.depthrg,
-                    process.out.depthsm,
-                    process.out.selfrg,
-                    process.out.selfsm,
-                    process.out.versions,
-                    ).match() }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["log"])).match() }
             )
         }
     }
 
+    test("test-verifybamid-verifybamid - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+				]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/genmod.vcf.gz', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
+
+
 }