nf-core-module-dev bots updating hmmer tools: hmmbuild, hmmsearch, hmmalign to topic versions and latest standards

modules/nf-core/hmmer/hmmalign/main.nf

@@ -4,16 +4,16 @@ process HMMER_HMMALIGN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/07/07c4cbd91c4459dc86b13b5cd799cacba96b27d66c276485550d299c7a4c6f8a/data' :
-        'community.wave.seqera.io/library/hmmer:3.4--cb5d2dd2e85974ca' }"
+        'https://depot.galaxyproject.org/singularity/hmmer:3.4--hb6cb901_4' :
+        'quay.io/biocontainers/hmmer:3.4--hb6cb901_4' }"
 
     input:
     tuple val(meta), path(fasta)
     path hmm
 
     output:
     tuple val(meta), path("*.sto.gz"), emit: sto
-    path "versions.yml"              , emit: versions
+    tuple val("${task.process}"), val("hmmer"), eval("hmmalign -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER //'"), topic: versions, emit: versions_hmmer
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,21 +26,11 @@ process HMMER_HMMALIGN {
         $args \\
         $hmm \\
         $fasta | gzip -c > ${prefix}.sto.gz
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        hmmer: \$(hmmalign -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER *//')
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    echo | gzip > ${prefix}.sto.gz
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        hmmer: \$(hmmalign -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER *//')
-    END_VERSIONS
+    echo "" | gzip > ${prefix}.sto.gz
     """
 }

modules/nf-core/hmmer/hmmalign/meta.yml

@@ -45,13 +45,29 @@ output:
           pattern: "*.sto.gz"
           ontologies:
             - edam: http://edamontology.org/format_3989 # GZIP format
+  versions_hmmer:
+    - - ${task.process}:
+          type: string
+          description: The process name
+      - hmmer:
+          type: string
+          description: The tool name
+      - hmmalign -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER //':
+          type: eval
+          description: The tool 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: The process name
+      - hmmer:
+          type: string
+          description: The tool name
+      - hmmalign -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER //':
+          type: eval
+          description: The tool version
+
 authors:
   - "@erikrikarddaniel"
   - "@jfy133"

modules/nf-core/hmmer/hmmalign/tests/main.nf.test

@@ -27,7 +27,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }
@@ -50,7 +50,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }

modules/nf-core/hmmer/hmmalign/tests/main.nf.test.snap

@@ -2,67 +2,53 @@
     "test-hmmer-hmmalign": {
         "content": [
             {
-                "0": [
+                "sto": [
                     [
                         {
                             "id": "test"
                         },
                         "test.sto.gz:md5,4ae989d5ade2aaae9578cb88ba031e8f"
                     ]
                 ],
-                "1": [
-                    "versions.yml:md5,601e13e7a1e6057766d862a828d501c4"
-                ],
-                "sto": [
+                "versions_hmmer": [
                     [
-                        {
-                            "id": "test"
-                        },
-                        "test.sto.gz:md5,4ae989d5ade2aaae9578cb88ba031e8f"
+                        "HMMER_HMMALIGN",
+                        "hmmer",
+                        "3.4"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,601e13e7a1e6057766d862a828d501c4"
                 ]
             }
         ],
+        "timestamp": "2026-05-01T15:54:13.981909183",
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "23.04.5"
-        },
-        "timestamp": "2024-11-13T12:37:26.551497424"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "test-hmmer-hmmalign-stub": {
         "content": [
             {
-                "0": [
+                "sto": [
                     [
                         {
                             "id": "test"
                         },
                         "test.sto.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
-                "1": [
-                    "versions.yml:md5,601e13e7a1e6057766d862a828d501c4"
-                ],
-                "sto": [
+                "versions_hmmer": [
                     [
-                        {
-                            "id": "test"
-                        },
-                        "test.sto.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "HMMER_HMMALIGN",
+                        "hmmer",
+                        "3.4"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,601e13e7a1e6057766d862a828d501c4"
                 ]
             }
         ],
+        "timestamp": "2026-05-01T15:54:21.354318795",
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "23.04.5"
-        },
-        "timestamp": "2024-11-13T12:37:32.244343836"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }

modules/nf-core/hmmer/hmmbuild/main.nf

@@ -4,8 +4,8 @@ process HMMER_HMMBUILD {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/07/07c4cbd91c4459dc86b13b5cd799cacba96b27d66c276485550d299c7a4c6f8a/data' :
-        'community.wave.seqera.io/library/hmmer:3.4--cb5d2dd2e85974ca' }"
+        'https://depot.galaxyproject.org/singularity/hmmer:3.4--hb6cb901_4' :
+        'quay.io/biocontainers/hmmer:3.4--hb6cb901_4' }"
 
     input:
     tuple val(meta), path(alignment)
@@ -14,7 +14,7 @@ process HMMER_HMMBUILD {
     output:
     tuple val(meta), path("*.hmm.gz"), emit: hmm
     path "*.hmmbuild.txt",             emit: hmmbuildout
-    path "versions.yml",               emit: versions
+    tuple val("${task.process}"), val("hmmer"), eval("hmmbuild -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER //'"), topic: versions, emit: versions_hmmer
 
     when:
     task.ext.when == null || task.ext.when
@@ -35,22 +35,12 @@ process HMMER_HMMBUILD {
         $alignment
 
     gzip ${prefix}.hmm
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        hmmer: \$(echo \$(hmmbuild -h | grep HMMER | sed 's/# HMMER //' | sed 's/ .*//' 2>&1))
-    END_VERSIONS
     """
 
     stub:
     def prefix    = task.ext.prefix ?: "${meta.id}"
     """
-    echo | gzip > ${prefix}.hmm.gz
+    echo "" | gzip > ${prefix}.hmm.gz
     touch ${prefix}.hmmbuild.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        hmmer: \$(echo \$(hmmbuild -h | grep HMMER | sed 's/# HMMER //' | sed 's/ .*//' 2>&1))
-    END_VERSIONS
     """
 }

modules/nf-core/hmmer/hmmbuild/meta.yml

@@ -36,10 +36,10 @@ input:
 output:
   hmm:
     - - meta:
-          type: file
-          description: Gzipped HMM file
-          pattern: "*.{hmm.gz}"
-          ontologies: []
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
       - "*.hmm.gz":
           type: file
           description: Gzipped HMM file
@@ -50,13 +50,29 @@ output:
         type: file
         description: HMM build output
         ontologies: []
+  versions_hmmer:
+    - - ${task.process}:
+          type: string
+          description: The process name
+      - hmmer:
+          type: string
+          description: The tool name
+      - hmmbuild -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER //':
+          type: eval
+          description: The tool 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: The process name
+      - hmmer:
+          type: string
+          description: The tool name
+      - hmmbuild -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER //':
+          type: eval
+          description: The tool version
+
 authors:
   - "@erikrikarddaniel"
 maintainers:

modules/nf-core/hmmer/hmmbuild/tests/main.nf.test

@@ -19,7 +19,7 @@ nextflow_process {
                                 [ id: 'PF14720' ], // meta map
                                 file(params.modules_testdata_base_path + 'delete_me/hmmer/PF14720_seed.alnfaa.gz', checkIfExists: true)
                             ]
-				input[1] = []
+                input[1] = []
 
                 """
             }
@@ -29,12 +29,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert file(process.out.hmmbuildout[0]).text.contains('CPU time:') },
-                { assert snapshot(
-					file(process.out.hmm[0][1]).name, // unstable
-					file(process.out.hmmbuildout[0]).name, // unstable
-					process.out.versions
-					).match()
-				}
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["hmm", "hmmbuildout"])).match() }
             )
         }
     }
@@ -49,7 +44,7 @@ nextflow_process {
                                 [ id: 'PF14720' ], // meta map
                                 file(params.modules_testdata_base_path + 'delete_me/hmmer/PF14720_seed.alnfaa.gz', checkIfExists: true)
                             ]
-				input[1] = []
+                input[1] = []
 
                 """
             }
@@ -58,7 +53,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }