Convert untar, pigz/compress, kallisto/index, samtools/index, bowtie2/build to topic versions

modules/nf-core/bowtie2/build/main.nf

@@ -12,7 +12,7 @@ process BOWTIE2_BUILD {
 
     output:
     tuple val(meta), path('bowtie2')    , emit: index
-    path "versions.yml"                 , emit: versions
+    tuple val("${task.process}"), val('bowtie2'), eval('bowtie2 --version 2>&1 | head -1 | sed "s/^.*bowtie2-align-s version //; s/ .*//"'), emit: versions_bowtie2, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,21 +22,12 @@ process BOWTIE2_BUILD {
     """
     mkdir bowtie2
     bowtie2-build $args --threads $task.cpus $fasta bowtie2/${fasta.baseName}
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
-    END_VERSIONS
     """
 
     stub:
     """
     mkdir bowtie2
     touch bowtie2/${fasta.baseName}.{1..4}.bt2
     touch bowtie2/${fasta.baseName}.rev.{1,2}.bt2
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
-    END_VERSIONS
     """
 }

modules/nf-core/bowtie2/build/meta.yml

@@ -1,31 +1,31 @@
 name: bowtie2_build
 description: Builds bowtie index for reference genome
 keywords:
-  - build
-  - index
-  - fasta
-  - genome
-  - reference
+- build
+- index
+- fasta
+- genome
+- reference
 tools:
-  - bowtie2:
-      description: |
-        Bowtie 2 is an ultrafast and memory-efficient tool for aligning
-        sequencing reads to long reference sequences.
-      homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
-      documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
-      doi: 10.1038/nmeth.1923
-      licence: ["GPL-3.0-or-later"]
-      identifier: ""
+- bowtie2:
+    description: |
+      Bowtie 2 is an ultrafast and memory-efficient tool for aligning
+      sequencing reads to long reference sequences.
+    homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
+    documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
+    doi: 10.1038/nmeth.1923
+    licence: ["GPL-3.0-or-later"]
+    identifier: ""
 input:
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing reference information
-          e.g. [ id:'test', single_end:false ]
-    - fasta:
-        type: file
-        description: Input genome fasta file
-        ontologies: []
+- - meta:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: Input genome fasta file
+      ontologies: []
 output:
   index:
     - - meta:
@@ -34,20 +34,36 @@ output:
             Groovy Map containing reference information
             e.g. [ id:'test', single_end:false ]
       - bowtie2:
-          type: file
+          type: directory
           description: Bowtie2 genome index files
           pattern: "*.bt2"
           ontologies: []
+  versions_bowtie2:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - bowtie2:
+          type: string
+          description: The name of the tool
+      - 'bowtie2 --version 2>&1 | head -1 | sed "s/^.*bowtie2-align-s version //; s/ .*//"':
+          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
+      - bowtie2:
+          type: string
+          description: The name of the tool
+      - 'bowtie2 --version 2>&1 | head -1 | sed "s/^.*bowtie2-align-s version //; s/ .*//"':
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
-  - "@joseespinosa"
-  - "@drpatelh"
+- "@joseespinosa"
+- "@drpatelh"
 maintainers:
-  - "@joseespinosa"
-  - "@drpatelh"
+- "@joseespinosa"
+- "@drpatelh"

modules/nf-core/bowtie2/build/tests/main.nf.test

@@ -22,8 +22,13 @@ nextflow_process {
         }
 
         then {
-            assert process.success
-            assert snapshot(process.out).match()
+            assertAll (
+                { assert process.success },
+                { assert snapshot(
+                    process.out.index,
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
+            )
         }
 
     }

modules/nf-core/bowtie2/build/tests/main.nf.test.snap

@@ -1,49 +1,35 @@
 {
     "Should run without failures": {
         "content": [
-            {
-                "0": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
                     [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            "genome.1.bt2:md5,cbe3d0bbea55bc57c99b4bfa25b5fbdf",
-                            "genome.2.bt2:md5,47b153cd1319abc88dda532462651fcf",
-                            "genome.3.bt2:md5,4ed93abba181d8dfab2e303e33114777",
-                            "genome.4.bt2:md5,c25be5f8b0378abf7a58c8a880b87626",
-                            "genome.rev.1.bt2:md5,52be6950579598a990570fbcf5372184",
-                            "genome.rev.2.bt2:md5,e3b4ef343dea4dd571642010a7d09597"
-                        ]
+                        "genome.1.bt2:md5,cbe3d0bbea55bc57c99b4bfa25b5fbdf",
+                        "genome.2.bt2:md5,47b153cd1319abc88dda532462651fcf",
+                        "genome.3.bt2:md5,4ed93abba181d8dfab2e303e33114777",
+                        "genome.4.bt2:md5,c25be5f8b0378abf7a58c8a880b87626",
+                        "genome.rev.1.bt2:md5,52be6950579598a990570fbcf5372184",
+                        "genome.rev.2.bt2:md5,e3b4ef343dea4dd571642010a7d09597"
                     ]
-                ],
-                "1": [
-                    "versions.yml:md5,d136fb9c16f0a9fb2ae804b2a5fbc09c"
-                ],
-                "index": [
+                ]
+            ],
+            {
+                "versions_bowtie2": [
                     [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            "genome.1.bt2:md5,cbe3d0bbea55bc57c99b4bfa25b5fbdf",
-                            "genome.2.bt2:md5,47b153cd1319abc88dda532462651fcf",
-                            "genome.3.bt2:md5,4ed93abba181d8dfab2e303e33114777",
-                            "genome.4.bt2:md5,c25be5f8b0378abf7a58c8a880b87626",
-                            "genome.rev.1.bt2:md5,52be6950579598a990570fbcf5372184",
-                            "genome.rev.2.bt2:md5,e3b4ef343dea4dd571642010a7d09597"
-                        ]
+                        "BOWTIE2_BUILD",
+                        "bowtie2",
+                        "2.5.4"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,d136fb9c16f0a9fb2ae804b2a5fbc09c"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.02.1"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2023-11-23T11:51:01.107681997"
+        "timestamp": "2026-01-28T17:52:30.165111"
     }
 }

modules/nf-core/kallisto/index/main.nf

@@ -12,7 +12,7 @@ process KALLISTO_INDEX {
 
     output:
     tuple val(meta), path("kallisto")  , emit: index
-    path "versions.yml"                , emit: versions
+    tuple val("${task.process}"), val('kallisto'), eval('kallisto 2>&1 | head -1 | sed "s/^kallisto //; s/Usage.*//"'), emit: versions_kallisto, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,20 +25,10 @@ process KALLISTO_INDEX {
         $args \\
         -i kallisto \\
         $fasta
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        kallisto: \$(echo \$(kallisto 2>&1) | sed 's/^kallisto //; s/Usage.*\$//')
-    END_VERSIONS
     """
 
     stub:
     """
     mkdir kallisto
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        kallisto: \$(echo \$(kallisto 2>&1) | sed 's/^kallisto //; s/Usage.*\$//')
-    END_VERSIONS
     """
 }

modules/nf-core/kallisto/index/meta.yml

@@ -6,9 +6,9 @@ keywords:
   - index
 tools:
   - kallisto:
-      description: Quantifying abundances of transcripts from bulk and single-cell RNA-Seq
-        data, or more generally of target sequences using high-throughput sequencing
-        reads.
+      description: Quantifying abundances of transcripts from bulk and single-cell
+        RNA-Seq data, or more generally of target sequences using high-throughput
+        sequencing reads.
       homepage: https://pachterlab.github.io/kallisto/
       documentation: https://pachterlab.github.io/kallisto/manual
       tool_dev_url: https://github.com/pachterlab/kallisto
@@ -36,13 +36,29 @@ output:
           type: directory
           description: Kallisto genome index
           pattern: "*.idx"
+  versions_kallisto:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - kallisto:
+          type: string
+          description: The name of the tool
+      - kallisto 2>&1 | head -1 | sed "s/^kallisto //; s/Usage.*//":
+          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
+      - kallisto:
+          type: string
+          description: The name of the tool
+      - kallisto 2>&1 | head -1 | sed "s/^kallisto //; s/Usage.*//":
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@ggabernet"
 maintainers:

modules/nf-core/kallisto/index/tests/main.nf.test

@@ -25,7 +25,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert path(process.out.index.get(0).get(1)).exists() },
-                { assert snapshot(process.out.versions).match() }
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match() }
             )
         }
     }
@@ -48,7 +48,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out.index,
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
             )
         }
     }