update module: PERBASE

modules/nf-core/perbase/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::perbase=1.0.0
+  - bioconda::perbase=1.2.0

modules/nf-core/perbase/main.nf

@@ -4,16 +4,16 @@ process PERBASE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5fad22cc063bd389d2a62d7710721cac547aff657c37be0f7afb4a66420b66/data':
-        'community.wave.seqera.io/library/perbase:1.0.0--913516700ed7b57e' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/cb/cbbc9b2585d5abbef69ca0b379353616e16c6b7b8aafdb0c8a2bee9c63747d8f/data':
+        'community.wave.seqera.io/library/perbase:1.2.0--8d7275913f5d0463' }"
 
     input:
     tuple val(meta) , path(bam)  , path(index), path(bed)
     tuple val(meta2), path(fasta), path(fai)
 
     output:
     tuple val(meta), path("*.tsv.gz"), emit: tsv
-    path "versions.yml"              , emit: versions
+    tuple val("${task.process}"), val('perbase'), eval('perbase --version |& sed "1!d ; s/perbase //"'), emit: versions_perbase, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -33,22 +33,12 @@ process PERBASE {
         --threads $task.cpus \\
         --bgzip \\
         --output ${prefix}.tsv.gz
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        perbase: \$(perbase --version |& sed '1!d ; s/perbase //')
-    END_VERSIONS
     """
 
     stub:
     def args   = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     echo "" | gzip > ${prefix}.tsv.gz
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        perbase: \$(perbase --version |& sed '1!d ; s/perbase //')
-    END_VERSIONS
     """
 }

modules/nf-core/perbase/meta.yml

@@ -1,4 +1,3 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "perbase"
 description: Per-base metrics on BAM/CRAM files.
 keywords:
@@ -37,8 +36,8 @@ input:
           - edam: "http://edamontology.org/format_3327"
     - bed:
         type: file
-        description: bed file containing regions of interest, where only bases
-          from the given regions will be reported
+        description: bed file containing regions of interest, where only bases from
+          the given regions will be reported
         pattern: "*.{bed}"
         ontologies:
           - edam: "http://edamontology.org/format_3003"
@@ -80,6 +79,29 @@ output:
 
         ontologies:
           - edam: http://edamontology.org/format_3750 # YAML
+  versions_perbase:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - perbase:
+          type: string
+          description: The name of the tool
+      - perbase --version |& sed "1!d ; s/perbase //":
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - perbase:
+          type: string
+          description: The name of the tool
+      - perbase --version |& sed "1!d ; s/perbase //":
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@camlloyd"
 maintainers: