Migrate shasum to topic channel versions and add stub block (#11400)

* Migrate shasum to topic channel versions and add stub block

- Converted versions.yml output to topic channel (versions_sha256sum)
- Removed END_VERSIONS heredoc from script block
- Added stub block with touch for .sha256 output
- Updated existing test to use sanitizeOutput(process.out)
- Added stub test case

Note: Tests pass on amd64 CI but fail locally on arm64
due to container being amd64-only (Wave container).

Contributes to #4570

* fix(shasum): fix bash quoting in eval() version command; update meta.yml via lint --fix; regenerate snap

* fix(shasum): switch from eval() to versions.yml+topic pattern

eval() with awk '{print $NF}' required double-escaped quotes that caused
process failures ('assert process.success' = false) in all CI runners.
Switch to versions.yml written in script and stub blocks.

* fix(maltextract): switch from eval() to versions.yml+topic pattern

eval() with sed 's/MaltExtract version//' required double-escaped single
quotes that caused 'Different Snapshot' failures in conda and singularity CI.
Switch to versions.yml written in script and stub blocks.

* fix(shasum): correct meta.yml to use type:file for path-based versions.yml topic emit

* chore(shasum): remove accidental maltextract change from this branch (scope isolation)

* fix(shasum): correct meta.yml versions_sha256sum to single-dash format (path not tuple)

* fix(shasum): replace versions.yml with topic channel eval output

* fix(shasum): correct meta.yml eval string and regenerate snapshot via docker profile

* fix(shasum): extract only version number in eval string

* fix(shasum): sync meta.yml eval string with main.nf

---------

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

Author: HReed1

modules/nf-core/shasum/main.nf

@@ -12,7 +12,7 @@ process SHASUM {
 
     output:
     tuple val(meta), path("*.sha256"), emit: checksum
-    path "versions.yml", emit: versions
+    tuple val("${task.process}"), val('sha256sum'), eval("sha256sum --version 2>&1 | head -n 1 | sed 's/.* //'"), emit: versions_sha256sum, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -24,10 +24,10 @@ process SHASUM {
         ${args} \\
         ${file} \\
         > ${file}.sha256
+    """
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        sha256sum: \$(echo \$(sha256sum --version 2>&1 | head -n 1| sed 's/^.*) //;' ))
-    END_VERSIONS
+    stub:
+    """
+    touch ${file}.sha256
     """
 }

modules/nf-core/shasum/meta.yml

@@ -9,7 +9,8 @@ tools:
       description: Create an SHA256 (256-bit) checksum.
       homepage: "https://www.gnu.org"
       documentation: "https://linux.die.net/man/1/shasum"
-      licence: ["GPLv3+"]
+      licence:
+        - "GPLv3+"
       identifier: ""
 input:
   - - meta:
@@ -34,13 +35,27 @@ output:
           description: File containing checksum
           pattern: "*.sha256"
           ontologies: []
+  versions_sha256sum:
+    - - ${task.process}:
+          type: string
+          description: Process name
+      - sha256sum:
+          type: string
+          description: Tool name
+      - "sha256sum --version 2>&1 | head -n 1 | sed 's/.* //'":
+          type: eval
+          description: Software version
+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: Process name
+      - sha256sum:
+          type: string
+          description: Tool name
+      - "sha256sum --version 2>&1 | head -n 1 | sed 's/.* //'":
+          type: eval
+          description: Software version
 authors:
   - "@matthdsm"
 maintainers:

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

@@ -15,9 +15,9 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-				    [ id:'test', single_end:false ], // meta map
-				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
-				]
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+                ]
 
                 """
             }
@@ -26,7 +26,31 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
+
+    test("test-shasum - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+                ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }

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

@@ -2,7 +2,7 @@
     "test-shasum": {
         "content": [
             {
-                "0": [
+                "checksum": [
                     [
                         {
                             "id": "test",
@@ -11,27 +11,46 @@
                         "test.paired_end.bam.sha256:md5,138a19e100f09fc975ea1b717da9b6dd"
                     ]
                 ],
-                "1": [
-                    "versions.yml:md5,9d5d3f7101eb83416b87a2d6d61a0fa5"
-                ],
+                "versions_sha256sum": [
+                    [
+                        "SHASUM",
+                        "sha256sum",
+                        "9.5"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-03T20:43:40.688253838",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "24.10.4"
+        }
+    },
+    "test-shasum - stub": {
+        "content": [
+            {
                 "checksum": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test.paired_end.bam.sha256:md5,138a19e100f09fc975ea1b717da9b6dd"
+                        "test.paired_end.bam.sha256:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,9d5d3f7101eb83416b87a2d6d61a0fa5"
+                "versions_sha256sum": [
+                    [
+                        "SHASUM",
+                        "sha256sum",
+                        "9.5"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-05-03T20:43:46.125782074",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
-        },
-        "timestamp": "2024-12-13T11:49:42.210020546"
+            "nf-test": "0.9.5",
+            "nextflow": "24.10.4"
+        }
     }
 }