Add Topic-based tool version capture to Trinity Module (#9273)

eit-maxlcummins · nvnieuwk · web-flow · commit 51cd38b007f8 · 2025-10-29T14:52:53.000+01:00
* add versions topic to trinity module

* add missing test for main.nf.test

* simplify string replacement for trinity version eval to remove use of colons - avoids potential yml clash

* update meta.yml to capture new version topics change

* add new test for aggregating versions via topic

* update snapshot for new tests

* Update modules/nf-core/trinity/meta.yml

remove leading space

Co-authored-by: Nicolas Vannieuwkerke &lt;101190534+nvnieuwk@users.noreply.github.com&gt;

---------

Co-authored-by: Nicolas Vannieuwkerke &lt;101190534+nvnieuwk@users.noreply.github.com&gt;
diff --git a/modules/nf-core/trinity/main.nf b/modules/nf-core/trinity/main.nf
@@ -14,7 +14,7 @@ process TRINITY {
     output:
     tuple val(meta), path("*.fa.gz")    , emit: transcript_fasta
     tuple val(meta), path("*.log")      , emit: log
-    path "versions.yml"                 , emit: versions
+    tuple val("${task.process}"), val('trinity'), eval("Trinity --version | grep 'Trinity version' | sed 's/.*Trinity-v//'"), topic: versions, emit: versions_trinity
 
     when:
     task.ext.when == null || task.ext.when
@@ -61,11 +61,6 @@ process TRINITY {
         > ${prefix}.fa.gz
 
     rm ${prefix}_trinity.Trinity.fasta
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        trinity: \$(Trinity --version | grep 'Trinity version:' | sed 's/Trinity version: Trinity-//')
-    END_VERSIONS
     """
 
     stub:
@@ -74,10 +69,5 @@ process TRINITY {
     touch ${prefix}.fa
     gzip ${prefix}.fa
     touch ${prefix}.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        trinity: \$(Trinity --version | grep 'Trinity version:' | sed 's/Trinity version: Trinity-//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/trinity/meta.yml b/modules/nf-core/trinity/meta.yml
@@ -51,13 +51,27 @@ output:
           description: Log from trinity
           pattern: "*.log"
           ontologies: []
-  versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+  versions_trinity:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - trinity:
+          type: string
+          description: The tool name
+      - Trinity --version | grep 'Trinity version' | sed 's/.*Trinity-v//':
+          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:
   - "@timslittle"
   - "@gallvp"
diff --git a/modules/nf-core/trinity/tests/main.nf.test b/modules/nf-core/trinity/tests/main.nf.test
@@ -30,7 +30,7 @@ nextflow_process {
                 { assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") },
                 { assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN7_c0_g1_i1 len=299 path=[0:0-151 2:152-298]") },
                 { assert snapshot(
-                    process.out.versions
+                    process.out.findAll { key, val -> key.startsWith("versions") }
                     ).match()
                 }
             )
@@ -57,7 +57,7 @@ nextflow_process {
                 { assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") },
                 { assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN10_c0_g1_i1 len=534 path=[0:0-533]") },
                 { assert snapshot(
-                    process.out.versions
+                    process.out.findAll { key, val -> key.startsWith("versions") }
                     ).match()
                 },
             )
@@ -87,7 +87,7 @@ nextflow_process {
                 { assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") },
                 { assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN12_c0_g1_i1 len=225 path=[0:0-224]") },
                 { assert snapshot(
-                    process.out.versions
+                    process.out.findAll { key, val -> key.startsWith("versions") }
                     ).match()
                 }
 
@@ -116,7 +116,7 @@ nextflow_process {
                 { assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") },
                 { assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN12_c0_g1_i1 len=268 path=[0:0-267]") },
                 { assert snapshot(
-                    process.out.versions
+                    process.out.findAll { key, val -> key.startsWith("versions") }
                     ).match()
                 }
             )
@@ -144,7 +144,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }
             )
         }
     }
diff --git a/modules/nf-core/trinity/tests/main.nf.test.snap b/modules/nf-core/trinity/tests/main.nf.test.snap
@@ -1,103 +1,92 @@
 {
     "homo_sapiens-test_rnaseq-paired-multiple": {
         "content": [
-            [
-                "versions.yml:md5,1c631aefa156e739b773679c471467c1"
-            ]
+            {
+                "versions_trinity": [
+                    [
+                        "TRINITY",
+                        "trinity",
+                        "2.15.2"
+                    ]
+                ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-11-28T14:08:11.163901364"
+        "timestamp": "2025-10-28T13:22:02.72961086"
     },
     "homo_sapiens-test_rnaseq-single": {
         "content": [
-            [
-                "versions.yml:md5,1c631aefa156e739b773679c471467c1"
-            ]
+            {
+                "versions_trinity": [
+                    [
+                        "TRINITY",
+                        "trinity",
+                        "2.15.2"
+                    ]
+                ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-11-28T14:07:10.975441404"
+        "timestamp": "2025-10-28T13:21:13.836913087"
     },
     "homo_sapiens-test_rnaseq-paired": {
         "content": [
-            [
-                "versions.yml:md5,1c631aefa156e739b773679c471467c1"
-            ]
+            {
+                "versions_trinity": [
+                    [
+                        "TRINITY",
+                        "trinity",
+                        "2.15.2"
+                    ]
+                ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-11-28T14:06:36.470824201"
+        "timestamp": "2025-10-28T13:20:45.185841704"
     },
     "homo_sapiens-test_rnaseq-single-multiple": {
         "content": [
-            [
-                "versions.yml:md5,1c631aefa156e739b773679c471467c1"
-            ]
+            {
+                "versions_trinity": [
+                    [
+                        "TRINITY",
+                        "trinity",
+                        "2.15.2"
+                    ]
+                ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-11-28T14:08:54.36318984"
+        "timestamp": "2025-10-28T13:22:38.810477312"
     },
     "homo_sapiens-test_rnaseq-stub": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,1c631aefa156e739b773679c471467c1"
-                ],
-                "log": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "transcript_fasta": [
+                "versions_trinity": [
                     [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "TRINITY",
+                        "trinity",
+                        "2.15.2"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,1c631aefa156e739b773679c471467c1"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-11-28T14:09:00.571900709"
+        "timestamp": "2025-10-28T13:49:50.612026008"
     }
-}
+}

Original file line number	Diff line number	Diff line change
`@@ -30,7 +30,7 @@ nextflow_process {`
`30`	`30`	`{ assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") },`
`31`	`31`	`{ assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN7_c0_g1_i1 len=299 path=[0:0-151 2:152-298]") },`
`32`	`32`	`{ assert snapshot(`
`33`		`- process.out.versions`
	`33`	`+ process.out.findAll { key, val -> key.startsWith("versions") }`
`34`	`34`	`).match()`
`35`	`35`	`}`
`36`	`36`	`)`
`@@ -57,7 +57,7 @@ nextflow_process {`
`57`	`57`	`{ assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") },`
`58`	`58`	`{ assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN10_c0_g1_i1 len=534 path=[0:0-533]") },`
`59`	`59`	`{ assert snapshot(`
`60`		`- process.out.versions`
	`60`	`+ process.out.findAll { key, val -> key.startsWith("versions") }`
`61`	`61`	`).match()`
`62`	`62`	`},`
`63`	`63`	`)`
`@@ -87,7 +87,7 @@ nextflow_process {`
`87`	`87`	`{ assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") },`
`88`	`88`	`{ assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN12_c0_g1_i1 len=225 path=[0:0-224]") },`
`89`	`89`	`{ assert snapshot(`
`90`		`- process.out.versions`
	`90`	`+ process.out.findAll { key, val -> key.startsWith("versions") }`
`91`	`91`	`).match()`
`92`	`92`	`}`
`93`	`93`
`@@ -116,7 +116,7 @@ nextflow_process {`
`116`	`116`	`{ assert path(process.out.log[0][1]).text.contains("All commands completed successfully.") },`
`117`	`117`	`{ assert path(process.out.transcript_fasta[0][1]).linesGzip.toString().contains(">TRINITY_DN12_c0_g1_i1 len=268 path=[0:0-267]") },`
`118`	`118`	`{ assert snapshot(`
`119`		`- process.out.versions`
	`119`	`+ process.out.findAll { key, val -> key.startsWith("versions") }`
`120`	`120`	`).match()`
`121`	`121`	`}`
`122`	`122`	`)`
`@@ -144,7 +144,7 @@ nextflow_process {`
`144`	`144`	`then {`
`145`	`145`	`assertAll(`
`146`	`146`	`{ assert process.success },`
`147`		`- { assert snapshot(process.out).match() }`
	`147`	`+ { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }`
`148`	`148`	`)`
`149`	`149`	`}`
`150`	`150`	`}`