use versions

Author: famosab

modules/nf-core/oncocnv/main.nf

@@ -66,8 +66,8 @@ process ONCOCNV {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         oncocnv: $VERSION
-        perl: \$(perl --version | grep 'This is perl' | sed 's/.*(v//g' | sed 's/)//g')
-        r: \$(R --version | grep "R version" | sed 's/R version //g')
+        perl: \$(perl --version | grep 'This is perl' | sed -E 's/.*v([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/')
+        r: \$(R --version | grep "R version" | sed -E 's/R version ([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/')
     END_VERSIONS
     """
 
@@ -82,8 +82,8 @@ process ONCOCNV {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         oncocnv: $VERSION
-        perl: \$(perl --version | grep 'This is perl' | sed 's/.*(v//g' | sed 's/)//g')
-        r: \$(R --version | grep "R version" | sed 's/R version //g')
+        perl: \$(perl --version | grep 'This is perl' | sed -E 's/.*v([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/')
+        r: \$(R --version | grep "R version" | sed -E 's/R version ([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/')
     END_VERSIONS
     """
 }

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

@@ -82,7 +82,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                    ).match() }
             )
         }
 

modules/nf-core/oncocnv/tests/main.nf.test.snap

@@ -30,7 +30,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,be20246b45f9c84d7625dcc76b8451f2"
+                    "versions.yml:md5,da4305b1e78b5eb47b932ac5b08be0ab"
                 ],
                 "png": [
                     [
@@ -60,42 +60,49 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,be20246b45f9c84d7625dcc76b8451f2"
+                    "versions.yml:md5,da4305b1e78b5eb47b932ac5b08be0ab"
                 ]
+            },
+            {
+                "ONCOCNV": {
+                    "oncocnv": 7.0,
+                    "perl": "5.30.0",
+                    "r": "3.6.3"
+                }
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-05-21T13:35:00.752831"
+        "timestamp": "2025-05-21T15:41:03.943617"
     },
     "human - bam": {
         "content": [
             {
                 "0": [
-
+                    
                 ],
                 "1": [
-
+                    
                 ],
                 "2": [
-
+                    
                 ],
                 "3": [
-
+                    
                 ],
                 "png": [
-
+                    
                 ],
                 "profile": [
-
+                    
                 ],
                 "summary": [
-
+                    
                 ],
                 "versions": [
-
+                    
                 ]
             }
         ],
@@ -105,4 +112,4 @@
         },
         "timestamp": "2025-05-21T13:34:52.08932"
     }
-}
+}