Migrate narfmap/hashtable to topic channels

modules/nf-core/narfmap/align/tests/main.nf.test

@@ -43,7 +43,7 @@ nextflow_process {
             assertAll (
                 { assert process.success },
                 { assert snapshot(
-                    process.out.bam,
+                    process.out.bam.collect { meta, bamFile -> [meta, file(bamFile).name, bam(bamFile).getHeaderMD5()] },
                     file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
                     process.out.findAll { key, val -> key.startsWith("versions") }
                 ).match()
@@ -73,7 +73,7 @@ nextflow_process {
             assertAll (
                 { assert process.success },
                 { assert snapshot(
-                    process.out.bam,
+                    process.out.bam.collect { meta, bamFile -> [meta, file(bamFile).name, bam(bamFile).getHeaderMD5()] },
                     file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
                     process.out.findAll { key, val -> key.startsWith("versions") }
                 ).match()
@@ -106,7 +106,7 @@ nextflow_process {
             assertAll (
                 { assert process.success },
                 { assert snapshot(
-                    process.out.bam,
+                    process.out.bam.collect { meta, bamFile -> [meta, file(bamFile).name, bam(bamFile).getHeaderMD5()] },
                     file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
                     process.out.findAll { key, val -> key.startsWith("versions") }
                 ).match()
@@ -139,7 +139,7 @@ nextflow_process {
             assertAll (
                 { assert process.success },
                 { assert snapshot(
-                    process.out.bam,
+                    process.out.bam.collect { meta, bamFile -> [meta, file(bamFile).name, bam(bamFile).getHeaderMD5()] },
                     file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
                     process.out.findAll { key, val -> key.startsWith("versions") }
                 ).match()
@@ -172,7 +172,7 @@ nextflow_process {
             assertAll (
                 { assert process.success },
                 { assert snapshot(
-                    process.out.bam,
+                    process.out.bam.collect { meta, bamFile -> [meta, file(bamFile).name, bam(bamFile).getHeaderMD5()] },
                     file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
                     process.out.findAll { key, val -> key.startsWith("versions") }
                 ).match()
@@ -207,7 +207,7 @@ nextflow_process {
             assertAll (
                 { assert process.success },
                 { assert snapshot(
-                    process.out.bam,
+                    process.out.bam.collect { meta, bamFile -> [meta, file(bamFile).name] },
                     file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
                     process.out.findAll { key, val -> key.startsWith("versions") }
                 ).match()

modules/nf-core/narfmap/align/tests/main.nf.test.snap

@@ -7,7 +7,8 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.bam:md5,05a72e1f017061967c1ecd95b4a11588"
+                    "test.bam",
+                    "aa68d3e5ae6049159a563b4ea76b4478"
                 ]
             ],
             [
@@ -42,10 +43,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-02-20T21:57:47.065808531",
+        "timestamp": "2026-08-03T17:28:06.089819887",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.2"
         }
     },
     "sarscov2 - [fastq1, fastq2], hashtable, true - stub": {
@@ -56,7 +57,7 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    "test.bam"
                 ]
             ],
             [
@@ -86,10 +87,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-02-20T21:57:55.043442298",
+        "timestamp": "2026-08-03T17:29:56.49662919",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.2"
         }
     },
     "sarscov2 - CRAM": {
@@ -143,7 +144,8 @@
                         "id": "test",
                         "single_end": true
                     },
-                    "test.bam:md5,3a275f59c824a956f234166274fe1049"
+                    "test.bam",
+                    "79e88aecfd62264a1018cf6cb47e7e39"
                 ]
             ],
             [
@@ -178,10 +180,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-02-20T21:57:11.280098551",
+        "timestamp": "2026-08-03T17:26:49.650528933",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.2"
         }
     },
     "sarscov2 - fastq, hashtable, true": {
@@ -192,7 +194,8 @@
                         "id": "test",
                         "single_end": true
                     },
-                    "test.bam:md5,af2401d3a72f278a9c3546ad77ee2a40"
+                    "test.bam",
+                    "58ccb538a46099fb73b47c76dd737bdc"
                 ]
             ],
             [
@@ -227,10 +230,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-02-20T21:57:19.604675313",
+        "timestamp": "2026-08-03T17:26:59.779346529",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.2"
         }
     },
     "sarscov2 - [fastq1, fastq2], hashtable, false": {
@@ -241,7 +244,8 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.bam:md5,908b56dc99a1ca58af4d7d13bcba454e"
+                    "test.bam",
+                    "dcbfd5628b07cd75b0885f97d15cdd38"
                 ]
             ],
             [
@@ -276,10 +280,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-02-20T21:57:28.156419739",
+        "timestamp": "2026-08-03T17:27:12.797643172",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.2"
         }
     },
     "sarscov2 - [fastq1, fastq2], hashtable, true": {
@@ -290,7 +294,8 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.bam:md5,05a72e1f017061967c1ecd95b4a11588"
+                    "test.bam",
+                    "aa68d3e5ae6049159a563b4ea76b4478"
                 ]
             ],
             [
@@ -325,10 +330,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-02-20T21:57:36.603419141",
+        "timestamp": "2026-08-03T17:27:26.864421081",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.2"
         }
     }
-}
+}

modules/nf-core/narfmap/align/tests/segfault.nf.test

@@ -44,9 +44,11 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
+                { assert process.out.bam.every { meta, bamFile -> file(bamFile).exists() } },
+                { assert process.out.bam.every { meta, bamFile -> file(bamFile).size() > 0 } },
+                { assert file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") } },
                 { assert snapshot(
-                    process.out.bam,
-                    file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
+                    process.out.bam.collect { meta, bamFile -> [meta, file(bamFile).name] },
                     process.out.findAll { key, val -> key.startsWith("versions") },
                 ).match()
                 }

modules/nf-core/narfmap/align/tests/segfault.nf.test.snap

@@ -7,17 +7,9 @@
                         "id": "test",
                         "single_end": true
                     },
-                    "test.bam:md5,4c3f0f32808e0b8e06b4bded09c1e17d"
+                    "test.bam"
                 ]
             ],
-            [
-                "decompHashTableCtxInit...",
-                "decompHashTableHeader...",
-                "decompHashTableLiterals...",
-                "decompHashTableExtIndex...",
-                "decompHashTableAutoHits...",
-                "decompHashTableSetFlags..."
-            ],
             {
                 "versions_narfmap": [
                     [
@@ -42,10 +34,10 @@
                 ]
             }
         ],
+        "timestamp": "2026-08-03T17:11:40.17375726",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
-        },
-        "timestamp": "2026-02-24T10:28:33.37180556"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.2"
+        }
     }
-}
+}

modules/nf-core/narfmap/hashtable/main.nf

@@ -11,8 +11,8 @@ process NARFMAP_HASHTABLE {
     tuple val(meta), path(fasta)
 
     output:
-    tuple val(meta), path("narfmap")    , emit: hashmap
-    path "versions.yml"                 , emit: versions
+    tuple val(meta), path("narfmap"), emit: hashmap
+    tuple val("${task.process}"), val('narfmap'), eval("dragen-os --version 2>&1"), emit: versions_narfmap, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,21 +27,11 @@ process NARFMAP_HASHTABLE {
         --output-directory narfmap \\
         $args \\
         --ht-num-threads $task.cpus
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        narfmap: \$(echo \$(dragen-os --version 2>&1))
-    END_VERSIONS
     """
 
     stub:
     """
     mkdir narfmap
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        narfmap: \$(echo \$(dragen-os --version 2>&1))
-    END_VERSIONS
     """
 
 }

modules/nf-core/narfmap/hashtable/meta.yml

@@ -35,13 +35,27 @@ output:
           description: NARFMAP hash table
           pattern: "*.{cmp,.bin,.txt}"
           ontologies: []
+  versions_narfmap:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - narfmap:
+          type: string
+          description: The name of the tool
+      - dragen-os --version 2>&1:
+          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
+      - narfmap:
+          type: string
+          description: The name of the tool
+      - dragen-os --version 2>&1:
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@edmundmiller"
 maintainers:

modules/nf-core/narfmap/hashtable/tests/main.nf.test

@@ -26,8 +26,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                        file(process.out.hashmap[0][1]).name,
-                        file(process.out.versions[0]).name
+                        sanitizeOutput(process.out, unstableKeys: ["hashmap"])
                     ).match()
                 }
             )
@@ -54,8 +53,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                        file(process.out.hashmap[0][1]).name,
-                        file(process.out.versions[0]).name
+                        sanitizeOutput(process.out, unstableKeys: ["hashmap"])
                     ).match()
                 }
             )