feat: update samtools sort module with version topic support

modules/nf-core/samtools/sort/main.nf

@@ -19,8 +19,8 @@ process SAMTOOLS_SORT {
     tuple val(meta), path("${prefix}.${extension}.crai"),   emit: crai, optional: true
     tuple val(meta), path("${prefix}.${extension}.csi"),    emit: csi,  optional: true
     tuple val(meta), path("${prefix}.${extension}.bai"),    emit: bai,  optional: true
-    path  "versions.yml",                                   emit: versions
-
+    tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools
+    
     when:
     task.ext.when == null || task.ext.when
 
@@ -53,10 +53,6 @@ process SAMTOOLS_SORT {
         -o ${output_file} \\
         -
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 
     stub:
@@ -77,10 +73,6 @@ process SAMTOOLS_SORT {
     """
     touch ${prefix}.${extension}
     ${index}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
+
     """
 }

modules/nf-core/samtools/sort/meta.yml

@@ -76,7 +76,6 @@ output:
           description: Sorted SAM file
           pattern: "*.{sam}"
           ontologies: []
-
   crai:
     - - meta:
           type: map
@@ -110,13 +109,28 @@ output:
           description: BAM index file (optional)
           pattern: "*.bai"
           ontologies: []
-  versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+  versions_samtools:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - samtools:
+          type: string
+          description: The tool name
+      - samtools version | sed '1!d;s/.* //':
+          type: string
+          description: The command used to generate the version of the tool
+
+topics:
+  - versions:
+      - - process:
+            type: string
+            description: The process the versions were collected from
+        - tool:
+            type: string
+            description: The tool name
+        - version:
+            type: string
+            description: The version of the tool
 authors:
   - "@drpatelh"
   - "@ewels"

modules/nf-core/samtools/sort/tests/main.nf.test

@@ -34,7 +34,7 @@ nextflow_process {
                 { assert snapshot(
                         process.out.bam,
                         process.out.bai,
-                        process.out.versions
+                        process.out.findAll { key, val -> key.startsWith("versions") }
                 ).match()}
             )
         }
@@ -66,7 +66,7 @@ nextflow_process {
                 { assert snapshot(
                         process.out.bam,
                         process.out.bai,
-                        process.out.versions
+                        process.out.findAll { key, val -> key.startsWith("versions") }
                 ).match()}
             )
         }
@@ -98,7 +98,7 @@ nextflow_process {
                 { assert snapshot(
                         process.out.bam,
                         process.out.csi,
-                        process.out.versions
+                        process.out.findAll { key, val -> key.startsWith("versions") }
                 ).match()}
             )
         }
@@ -133,7 +133,7 @@ nextflow_process {
                 { assert snapshot(
                         process.out.bam,
                         process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } },
-                        process.out.versions
+                        process.out.findAll { key, val -> key.startsWith("versions") }
                 ).match()}
             )
         }
@@ -168,7 +168,7 @@ nextflow_process {
                 { assert snapshot(
                         process.out.bam,
                         process.out.bai.collect { it.collect { it instanceof Map ? it : file(it).name } },
-                        process.out.versions
+                        process.out.findAll { key, val -> key.startsWith("versions") }
                 ).match()}
             )
         }
@@ -203,7 +203,7 @@ nextflow_process {
                 { assert snapshot(
                         process.out.bam,
                         process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } },
-                        process.out.versions
+                        process.out.findAll { key, val -> key.startsWith("versions") }
                 ).match()}
             )
         }
@@ -235,7 +235,7 @@ nextflow_process {
                 { assert snapshot(
                     process.out.cram.collect { it.collect { it instanceof Map ? it : file(it).name } },
                     process.out.crai.collect { it.collect { it instanceof Map ? it : file(it).name } },
-                    process.out.versions
+                    process.out.findAll { key, val -> key.startsWith("versions") }
                 ).match()}
             )
         }
@@ -265,7 +265,7 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }
             )
         }
     }
@@ -296,7 +296,7 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }
             )
         }
     }
@@ -325,7 +325,7 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }
             )
         }
     }