Update to topic preseq

modules/nf-core/preseq/ccurve/main.nf

@@ -14,7 +14,7 @@ process PRESEQ_CCURVE {
     output:
     tuple val(meta), path("*.c_curve.txt"), emit: c_curve
     tuple val(meta), path("*.log")        , emit: log
-    path "versions.yml"                   , emit: versions
+    tuple val("${task.process}"), val('preseq'), eval("preseq 2>&1 | sed -n 's/Version: //p'"), emit: versions_preseq, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,27 +26,17 @@ process PRESEQ_CCURVE {
     """
     preseq \\
         c_curve \\
-        $args \\
-        $paired_end \\
+        ${args} \\
+        ${paired_end} \\
         -output ${prefix}.c_curve.txt \\
-        $bam
+        ${bam}
     cp .command.err ${prefix}.command.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        preseq: \$(echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//')
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.c_curve.txt
     touch ${prefix}.command.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        preseq: \$(echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//')
-    END_VERSIONS
     """
 }

modules/nf-core/preseq/ccurve/meta.yml

@@ -1,18 +1,17 @@
 name: preseq_ccurve
-description: Software for predicting library complexity and genome coverage in high-throughput
-  sequencing
+description: Software for predicting library complexity and genome coverage in high-throughput sequencing
 keywords:
   - preseq
   - library
   - complexity
 tools:
   - preseq:
-      description: Software for predicting library complexity and genome coverage in
-        high-throughput sequencing
+      description: Software for predicting library complexity and genome coverage in high-throughput sequencing
       homepage: http://smithlabresearch.org/software/preseq/
       documentation: http://smithlabresearch.org/wp-content/uploads/manual.pdf
       tool_dev_url: https://github.com/smithlabcode/preseq
-      licence: ["GPL"]
+      licence:
+        - "GPL"
       identifier: biotools:preseq
 input:
   - - meta:
@@ -48,13 +47,29 @@ output:
           description: Log file containing stderr produced by Preseq
           pattern: "*.{log}"
           ontologies: []
+  versions_preseq:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - preseq:
+          type: string
+          description: The name of the tool
+      - "preseq 2>&1 | sed -n 's/Version: //p'":
+          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
+      - preseq:
+          type: string
+          description: The name of the tool
+      - "preseq 2>&1 | sed -n 's/Version: //p'":
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@drpatelh"
   - "@edmundmiller"

modules/nf-core/preseq/ccurve/tests/main.nf.test

@@ -11,78 +11,62 @@ nextflow_process {
     tag "preseq/ccurve"
 
     test("test-preseq-ccurve-single-end") {
-
         when {
             process {
                 """
                 input[0] = [
-				    [ id:'test', single_end:false ], // meta map
+				    [ id:'test', single_end:false ],
 				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
 				]
-
                 """
             }
         }
 
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-					process.out.c_curve,
-					file(process.out.log[0][1]).name,
-					process.out.versions
-					).match()
-				}
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys:["log"])).match() }
             )
         }
     }
 
     test("test-preseq-ccurve-paired-end") {
-
         when {
             process {
                 """
                 input[0] = [
-				    [ id:'test', single_end:false ], // meta map
+				    [ id:'test', single_end:false ],
 				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
 				]
-
                 """
             }
         }
 
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-					process.out.c_curve,
-					file(process.out.log[0][1]).name,
-					process.out.versions
-					).match()
-				}
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys:["log"])).match() }
             )
         }
     }
 
     test("test-preseq-ccurve-paired-end-stub") {
         options '-stub'
-
         when {
             process {
                 """
                 input[0] = [
-				    [ id:'test', single_end:false ], // meta map
+				    [ id:'test', single_end:false ],
 				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
 				]
-
                 """
             }
         }
 
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }

modules/nf-core/preseq/ccurve/tests/main.nf.test.snap

@@ -1,72 +1,79 @@
 {
     "test-preseq-ccurve-paired-end": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.c_curve.txt:md5,cf4743abdd355595d6ec1fb3f38e66e5"
+            {
+                "c_curve": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.c_curve.txt:md5,cf4743abdd355595d6ec1fb3f38e66e5"
+                    ]
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.command.log"
+                    ]
+                ],
+                "versions_preseq": [
+                    [
+                        "PRESEQ_CCURVE",
+                        "preseq",
+                        "3.2.0"
+                    ]
                 ]
-            ],
-            "test.command.log",
-            [
-                "versions.yml:md5,2702c580fbb9fbe70468c50c9948aa29"
-            ]
+            }
         ],
+        "timestamp": "2026-08-06T18:55:27.240838543",
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-10-19T17:07:03.336886334"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
     },
     "test-preseq-ccurve-single-end": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.c_curve.txt:md5,cf4743abdd355595d6ec1fb3f38e66e5"
-                ]
-            ],
-            "test.command.log",
-            [
-                "versions.yml:md5,2702c580fbb9fbe70468c50c9948aa29"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-10-19T17:06:51.412629669"
-    },
-    "test-preseq-ccurve-paired-end-stub": {
         "content": [
             {
-                "0": [
+                "c_curve": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test.c_curve.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.c_curve.txt:md5,cf4743abdd355595d6ec1fb3f38e66e5"
                     ]
                 ],
-                "1": [
+                "log": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test.command.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.command.log"
                     ]
                 ],
-                "2": [
-                    "versions.yml:md5,2702c580fbb9fbe70468c50c9948aa29"
-                ],
+                "versions_preseq": [
+                    [
+                        "PRESEQ_CCURVE",
+                        "preseq",
+                        "3.2.0"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-08-06T18:55:20.969801086",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
+    },
+    "test-preseq-ccurve-paired-end-stub": {
+        "content": [
+            {
                 "c_curve": [
                     [
                         {
@@ -85,15 +92,19 @@
                         "test.command.log:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,2702c580fbb9fbe70468c50c9948aa29"
+                "versions_preseq": [
+                    [
+                        "PRESEQ_CCURVE",
+                        "preseq",
+                        "3.2.0"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-08-06T18:55:33.242745598",
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-10-19T17:07:21.526898235"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
     }
 }

modules/nf-core/preseq/lcextrap/main.nf

@@ -14,7 +14,7 @@ process PRESEQ_LCEXTRAP {
     output:
     tuple val(meta), path("*.lc_extrap.txt"), emit: lc_extrap
     tuple val(meta), path("*.log")          , emit: log
-    tuple val("${task.process}"), val('preseq'), eval("preseq 2>&1 | sed -n 's/.*Version: \\(.*\\)/\\1/p'"), emit: versions_preseq, topic: versions
+    tuple val("${task.process}"), val('preseq'), eval("preseq 2>&1 | sed -n 's/Version: //p'"), emit: versions_preseq, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,10 +27,10 @@ process PRESEQ_LCEXTRAP {
     """
     preseq \\
         lc_extrap \\
-        $args \\
-        $paired_end \\
+        ${args} \\
+        ${paired_end} \\
         -output ${prefix}.lc_extrap.txt \\
-        $bam
+        ${bam}
     cp .command.err ${prefix}.command.log
     """
 

modules/nf-core/preseq/lcextrap/meta.yml

@@ -1,18 +1,17 @@
 name: preseq_lcextrap
-description: Software for predicting library complexity and genome coverage in high-throughput
-  sequencing
+description: Software for predicting library complexity and genome coverage in high-throughput sequencing
 keywords:
   - preseq
   - library
   - complexity
 tools:
   - preseq:
-      description: Software for predicting library complexity and genome coverage in
-        high-throughput sequencing
+      description: Software for predicting library complexity and genome coverage in high-throughput sequencing
       homepage: http://smithlabresearch.org/software/preseq/
       documentation: http://smithlabresearch.org/wp-content/uploads/manual.pdf
       tool_dev_url: https://github.com/smithlabcode/preseq
-      licence: ["GPL"]
+      licence:
+        - "GPL"
       identifier: biotools:preseq
 input:
   - - meta:
@@ -55,7 +54,7 @@ output:
       - preseq:
           type: string
           description: The name of the tool
-      - "preseq 2>&1 | sed -n 's/.*Version: \\(.*\\)/\\1/p'":
+      - "preseq 2>&1 | sed -n 's/Version: //p'":
           type: eval
           description: The expression to obtain the version of the tool
 
@@ -67,7 +66,7 @@ topics:
       - preseq:
           type: string
           description: The name of the tool
-      - "preseq 2>&1 | sed -n 's/.*Version: \\(.*\\)/\\1/p'":
+      - "preseq 2>&1 | sed -n 's/Version: //p'":
           type: eval
           description: The expression to obtain the version of the tool