Update all hAMRonization modules to latest version (#9171)

* Add new input channel for premade seqid2map file

* Add extra tests for using custom seqid2map file

* Apply suggestions from code review

* Update modules/nf-core/kraken2/build/tests/main.nf.test

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

* update all hAMRonization modules to latest version

---------

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

Author: jfy133

modules/nf-core/hamronization/abricate/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::hamronization=1.1.4
+  - bioconda::hamronization=1.1.9

modules/nf-core/hamronization/abricate/main.nf

@@ -1,22 +1,22 @@
 process HAMRONIZATION_ABRICATE {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/hamronization:1.1.4--pyhdfd78af_0':
-        'biocontainers/hamronization:1.1.4--pyhdfd78af_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/hamronization:1.1.9--pyhdfd78af_0'
+        : 'biocontainers/hamronization:1.1.9--pyhdfd78af_0'}"
 
     input:
     tuple val(meta), path(report)
-    val(format)
-    val(software_version)
-    val(reference_db_version)
+    val format
+    val software_version
+    val reference_db_version
 
     output:
     tuple val(meta), path("*.json"), optional: true, emit: json
-    tuple val(meta), path("*.tsv") , optional: true, emit: tsv
-    path "versions.yml"            , emit: versions
+    tuple val(meta), path("*.tsv"), optional: true, emit: tsv
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -28,7 +28,7 @@ process HAMRONIZATION_ABRICATE {
     hamronize \\
         abricate \\
         ${report} \\
-        $args \\
+        ${args} \\
         --format ${format} \\
         --analysis_software_version ${software_version} \\
         --reference_database_version ${reference_db_version} \\

modules/nf-core/hamronization/abricate/tests/main.nf.test.snap

@@ -14,7 +14,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,c826615ee7b88b615cae5bded792b790"
+                    "versions.yml:md5,113fee72fb15d06692b7fc29ee477aff"
                 ],
                 "json": [
 
@@ -28,15 +28,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c826615ee7b88b615cae5bded792b790"
+                    "versions.yml:md5,113fee72fb15d06692b7fc29ee477aff"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2024-02-07T22:16:18.968989666"
+        "timestamp": "2025-10-04T06:44:38.664437882"
     },
     "hamronization/abricate - bacteroides_fragilis - genome_abricate_tsv - stub": {
         "content": [
@@ -53,7 +53,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,c826615ee7b88b615cae5bded792b790"
+                    "versions.yml:md5,113fee72fb15d06692b7fc29ee477aff"
                 ],
                 "json": [
 
@@ -67,14 +67,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c826615ee7b88b615cae5bded792b790"
+                    "versions.yml:md5,113fee72fb15d06692b7fc29ee477aff"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2024-02-07T22:25:57.524839789"
+        "timestamp": "2025-10-04T06:44:45.131612041"
     }
 }

modules/nf-core/hamronization/amrfinderplus/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::hamronization=1.1.4
+  - bioconda::hamronization=1.1.9

modules/nf-core/hamronization/amrfinderplus/main.nf

@@ -1,22 +1,22 @@
 process HAMRONIZATION_AMRFINDERPLUS {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/hamronization:1.1.4--pyhdfd78af_0':
-        'biocontainers/hamronization:1.1.4--pyhdfd78af_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/hamronization:1.1.9--pyhdfd78af_0'
+        : 'biocontainers/hamronization:1.1.9--pyhdfd78af_0'}"
 
     input:
     tuple val(meta), path(report)
-    val(format)
-    val(software_version)
-    val(reference_db_version)
+    val format
+    val software_version
+    val reference_db_version
 
     output:
-    tuple val(meta), path("*.json") , optional: true, emit: json
-    tuple val(meta), path("*.tsv")  , optional: true, emit: tsv
-    path "versions.yml"                             , emit: versions
+    tuple val(meta), path("*.json"), optional: true, emit: json
+    tuple val(meta), path("*.tsv"), optional: true, emit: tsv
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -28,7 +28,7 @@ process HAMRONIZATION_AMRFINDERPLUS {
     hamronize \\
         amrfinderplus \\
         ${report} \\
-        $args \\
+        ${args} \\
         --format ${format} \\
         --analysis_software_version ${software_version} \\
         --reference_database_version ${reference_db_version} \\

modules/nf-core/hamronization/amrfinderplus/tests/main.nf.test

@@ -16,11 +16,11 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map                                                                                                                           
-                    file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/amrfinderplus/test_output.tsv", checkIfExists: true)                              
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/amrfinderplus/test_output_prot.tsv", checkIfExists: true)                              
                 ]
                 input[1] = 'tsv'
-                input[2] = '3.10.30'
-                input[3] = '2022-05-26.1'
+                input[2] = '4.0.23'
+                input[3] = '2025-07-16.1'
                 """
             }
         }
@@ -43,11 +43,11 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map                                                                                                                           
-                    file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/amrfinderplus/test_output.tsv", checkIfExists: true)                              
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/amrfinderplus/test_output_prot.tsv", checkIfExists: true)                              
                 ]
                 input[1] = 'tsv'
-                input[2] = '3.10.30'
-                input[3] = '2022-05-26.1'
+                input[2] = '4.0.23'
+                input[3] = '2025-07-16.1'
                 """
             }
         }

modules/nf-core/hamronization/amrfinderplus/tests/main.nf.test.snap

@@ -15,7 +15,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,8a2099aeaf76a6cacfca285faa389257"
+                    "versions.yml:md5,bb043ef684cba407b418320169e43fca"
                 ],
                 "json": [
 
@@ -30,15 +30,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,8a2099aeaf76a6cacfca285faa389257"
+                    "versions.yml:md5,bb043ef684cba407b418320169e43fca"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2024-02-07T10:47:35.965140591"
+        "timestamp": "2025-10-04T06:44:58.153879797"
     },
     "hamronization/amrfinderplus - delete_me/amrfinderplus - tsv": {
         "content": [
@@ -52,11 +52,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.tsv:md5,cde9a32a5b0a8902c4a76ebd2a820d4d"
+                        "test.tsv:md5,129da2f25d4d68ab106990f1ae31d999"
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,8a2099aeaf76a6cacfca285faa389257"
+                    "versions.yml:md5,bb043ef684cba407b418320169e43fca"
                 ],
                 "json": [
 
@@ -67,18 +67,18 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.tsv:md5,cde9a32a5b0a8902c4a76ebd2a820d4d"
+                        "test.tsv:md5,129da2f25d4d68ab106990f1ae31d999"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,8a2099aeaf76a6cacfca285faa389257"
+                    "versions.yml:md5,bb043ef684cba407b418320169e43fca"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2024-02-07T10:47:30.194755603"
+        "timestamp": "2025-10-04T07:43:32.220753935"
     }
 }

modules/nf-core/hamronization/deeparg/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::hamronization=1.1.4
+  - bioconda::hamronization=1.1.9

modules/nf-core/hamronization/deeparg/main.nf

@@ -1,22 +1,22 @@
 process HAMRONIZATION_DEEPARG {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/hamronization:1.1.4--pyhdfd78af_0':
-        'biocontainers/hamronization:1.1.4--pyhdfd78af_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/hamronization:1.1.9--pyhdfd78af_0'
+        : 'biocontainers/hamronization:1.1.9--pyhdfd78af_0'}"
 
     input:
     tuple val(meta), path(report)
-    val(format)
-    val(software_version)
-    val(reference_db_version)
+    val format
+    val software_version
+    val reference_db_version
 
     output:
     tuple val(meta), path("*.json"), optional: true, emit: json
-    tuple val(meta), path("*.tsv") , optional: true, emit: tsv
-    path "versions.yml"            , emit: versions
+    tuple val(meta), path("*.tsv"), optional: true, emit: tsv
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -28,7 +28,7 @@ process HAMRONIZATION_DEEPARG {
     hamronize \\
         deeparg \\
         ${report} \\
-        $args \\
+        ${args} \\
         --format ${format} \\
         --analysis_software_version ${software_version} \\
         --reference_database_version ${reference_db_version} \\

modules/nf-core/hamronization/deeparg/tests/main.nf.test.snap

@@ -15,7 +15,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,2f75284447982578412e05eb09c5367f"
+                    "versions.yml:md5,e574e91477c7753e96c2e8411419cec1"
                 ],
                 "json": [
 
@@ -30,15 +30,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,2f75284447982578412e05eb09c5367f"
+                    "versions.yml:md5,e574e91477c7753e96c2e8411419cec1"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2024-02-08T00:43:44.834346159"
+        "timestamp": "2025-10-04T06:45:13.092217921"
     },
     "hamronization/deeparg - bacteroides_fragilis - genome_mapping_potential_arg": {
         "content": [
@@ -56,7 +56,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,2f75284447982578412e05eb09c5367f"
+                    "versions.yml:md5,e574e91477c7753e96c2e8411419cec1"
                 ],
                 "json": [
 
@@ -71,14 +71,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,2f75284447982578412e05eb09c5367f"
+                    "versions.yml:md5,e574e91477c7753e96c2e8411419cec1"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2024-02-07T10:32:36.722182719"
+        "timestamp": "2025-10-04T06:45:06.201275925"
     }
 }