Make rundbcan/easysybstract synteny_pdf as optional, version topics upgrade, bump version

modules/nf-core/rundbcan/cazymeannotation/environment.yml

@@ -4,4 +4,4 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - bioconda::dbcan=5.2.6
+  - bioconda::dbcan=5.2.8

modules/nf-core/rundbcan/cazymeannotation/main.nf

@@ -1,22 +1,22 @@
 process RUNDBCAN_CAZYMEANNOTATION {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/dbcan:5.2.6--pyhdfd78af_0' :
-        'quay.io/biocontainers/dbcan:5.2.6--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/dbcan:5.2.8--pyhdfd78af_0' :
+        'quay.io/biocontainers/dbcan:5.2.8--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(input_raw_data)
     path dbcan_db
 
     output:
-    tuple val(meta), path("${prefix}_overview.tsv")            , emit: cazyme_annotation
-    tuple val(meta), path("${prefix}_dbCAN_hmm_results.tsv")   , emit: dbcanhmm_results
+    tuple val(meta), path("${prefix}_overview.tsv"), emit: cazyme_annotation
+    tuple val(meta), path("${prefix}_dbCAN_hmm_results.tsv"), emit: dbcanhmm_results
     tuple val(meta), path("${prefix}_dbCANsub_hmm_results.tsv"), emit: dbcansub_results
-    tuple val(meta), path("${prefix}_diamond.out")             , emit: dbcandiamond_results
-    path  "versions.yml"                                       , emit: versions
+    tuple val(meta), path("${prefix}_diamond.out"), emit: dbcandiamond_results
+    tuple val("${task.process}"), val('rundbcan'), eval("run_dbcan version | sed 's/dbCAN version: //g'"), emit: versions_rundbcan, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -36,11 +36,6 @@ process RUNDBCAN_CAZYMEANNOTATION {
     mv dbCAN_hmm_results.tsv ${prefix}_dbCAN_hmm_results.tsv
     mv dbCANsub_hmm_results.tsv ${prefix}_dbCANsub_hmm_results.tsv
     mv diamond.out ${prefix}_diamond.out
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        dbcan: \$(echo \$(run_dbcan version) | cut -f2 -d':' | cut -f2 -d' ')
-    END_VERSIONS
     """
 
     stub:
@@ -50,10 +45,5 @@ process RUNDBCAN_CAZYMEANNOTATION {
     touch ${prefix}_dbCAN_hmm_results.tsv
     touch ${prefix}_dbCANsub_hmm_results.tsv
     touch ${prefix}_diamond.out
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        dbcan: \$(echo \$(run_dbcan version) | cut -f2 -d':' | cut -f2 -d' ')
-    END_VERSIONS
     """
 }

modules/nf-core/rundbcan/cazymeannotation/meta.yml

@@ -1,8 +1,7 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "rundbcan_cazymeannotation"
-description: CAZyme annotation module for the dbcan pipeline. This module is used
-  to annotate carbohydrate-active enzymes (CAZymes) from genomic data using the dbCAN
-  annotation tool.
+description: CAZyme annotation module for the dbcan pipeline. This module is
+  used to annotate carbohydrate-active enzymes (CAZymes) from genomic data using
+  the dbCAN annotation tool.
 keywords:
   - dbCAN
   - download
@@ -17,9 +16,9 @@ tools:
       documentation: "https://run-dbcan.readthedocs.io/en/latest/"
       tool_dev_url: "https://github.com/bcb-unl/run_dbcan"
       doi: "10.1093/nar/gkad328"
-      licence: ["GPL v3-or-later"]
+      licence:
+        - "GPL v3-or-later"
       identifier: biotools:dbcan
-
 input:
   - - meta:
         type: map
@@ -31,8 +30,8 @@ input:
         description: FASTA file for protein sequences.
         pattern: "*.{fasta,fa,faa}"
         ontologies:
-          - edam: "http://edamontology.org/data_2044" # Sequence
-          - edam: "http://edamontology.org/format_1929" # FASTA
+          - edam: "http://edamontology.org/data_2044"
+          - edam: "http://edamontology.org/format_1929"
   - dbcan_db:
       type: directory
       description: Path to the dbCAN database directory.
@@ -81,13 +80,27 @@ output:
           description: |
             TSV file containing the detailed dbCAN diamond results for CAZyme annotation.
           ontologies: []
+  versions_rundbcan:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - rundbcan:
+          type: string
+          description: The name of the tool
+      - "run_dbcan version | sed 's/dbCAN version: //g'":
+          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
+      - rundbcan:
+          type: string
+          description: The name of the tool
+      - "run_dbcan version | sed 's/dbCAN version: //g'":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@Xinpeng021001"
 maintainers:

modules/nf-core/rundbcan/cazymeannotation/tests/main.nf.test

@@ -37,10 +37,7 @@ nextflow_process {
         then {
             assert process.success
             assertAll(
-                { assert snapshot(
-                    process.out,
-                    path(process.out.versions[0]).yaml
-                    ).match()
+                { assert snapshot(process.out).match()
                 }
             )
         }
@@ -61,10 +58,7 @@ nextflow_process {
         then {
             assert process.success
             assertAll(
-                { assert snapshot(
-                    process.out,
-                    path(process.out.versions[0]).yaml
-                    ).match()
+                { assert snapshot(process.out).match()
                 }
             )
         }

modules/nf-core/rundbcan/cazymeannotation/tests/main.nf.test.snap

@@ -35,7 +35,11 @@
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,51c852df9519c8781977cf96a01dfc6a"
+                    [
+                        "RUNDBCAN_CAZYMEANNOTATION",
+                        "rundbcan",
+                        "5.2.8"
+                    ]
                 ],
                 "cazyme_annotation": [
                     [
@@ -69,21 +73,20 @@
                         "stub_dbCANsub_hmm_results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,51c852df9519c8781977cf96a01dfc6a"
+                "versions_rundbcan": [
+                    [
+                        "RUNDBCAN_CAZYMEANNOTATION",
+                        "rundbcan",
+                        "5.2.8"
+                    ]
                 ]
-            },
-            {
-                "RUNDBCAN_CAZYMEANNOTATION": {
-                    "dbcan": "5.2.6"
-                }
             }
         ],
+        "timestamp": "2026-04-20T12:23:30.010346172",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2026-02-02T13:06:18.515911731"
+            "nf-test": "0.9.5",
+            "nextflow": "24.10.3"
+        }
     },
     "dbcancazyme - simplified": {
         "content": [
@@ -121,7 +124,11 @@
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,51c852df9519c8781977cf96a01dfc6a"
+                    [
+                        "RUNDBCAN_CAZYMEANNOTATION",
+                        "rundbcan",
+                        "5.2.8"
+                    ]
                 ],
                 "cazyme_annotation": [
                     [
@@ -155,20 +162,19 @@
                         "test_dbCANsub_hmm_results.tsv:md5,d771df5ab5b2967ced24c04fe54abf17"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,51c852df9519c8781977cf96a01dfc6a"
+                "versions_rundbcan": [
+                    [
+                        "RUNDBCAN_CAZYMEANNOTATION",
+                        "rundbcan",
+                        "5.2.8"
+                    ]
                 ]
-            },
-            {
-                "RUNDBCAN_CAZYMEANNOTATION": {
-                    "dbcan": "5.2.6"
-                }
             }
         ],
+        "timestamp": "2026-04-20T12:23:24.276249869",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2026-02-02T13:06:15.732926016"
+            "nf-test": "0.9.5",
+            "nextflow": "24.10.3"
+        }
     }
 }

modules/nf-core/rundbcan/database/environment.yml

@@ -4,4 +4,4 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - bioconda::dbcan=5.2.6
+  - bioconda::dbcan=5.2.8

modules/nf-core/rundbcan/database/main.nf

@@ -3,12 +3,12 @@ process RUNDBCAN_DATABASE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/dbcan:5.2.6--pyhdfd78af_0' :
-        'quay.io/biocontainers/dbcan:5.2.6--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/dbcan:5.2.8--pyhdfd78af_0' :
+        'quay.io/biocontainers/dbcan:5.2.8--pyhdfd78af_0' }"
 
     output:
-    path "dbcan_db"    , emit: dbcan_db
-    path "versions.yml", emit: versions
+    path "dbcan_db", emit: dbcan_db
+    tuple val("${task.process}"), val('rundbcan'), eval("run_dbcan version | sed 's/dbCAN version: //g'"), emit: versions_rundbcan, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -18,20 +18,10 @@ process RUNDBCAN_DATABASE {
     run_dbcan database \\
         --db_dir dbcan_db \\
         --aws_s3
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        dbcan: \$(echo \$(run_dbcan version) | cut -f2 -d':' | cut -f2 -d' ')
-    END_VERSIONS
     """
 
     stub:
     """
     mkdir -p dbcan_db
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        dbcan: \$(echo \$(run_dbcan version) | cut -f2 -d':' | cut -f2 -d' ')
-    END_VERSIONS
     """
 }

modules/nf-core/rundbcan/database/meta.yml

@@ -1,6 +1,6 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "rundbcan_database"
-description: command from run_dbcan to prepare the database for dbCAN annotation.
+description: command from run_dbcan to prepare the database for dbCAN
+  annotation.
 keywords:
   - dbCAN
   - download
@@ -15,23 +15,37 @@ tools:
       documentation: "https://run-dbcan.readthedocs.io/en/latest/"
       tool_dev_url: "https://github.com/bcb-unl/run_dbcan"
       doi: "10.1093/nar/gkad328"
-      licence: ["GPL v3-or-later"]
+      licence:
+        - "GPL v3-or-later"
       identifier: biotools:dbcan
-
+input: []
 output:
   dbcan_db:
     - dbcan_db:
         type: directory
         description: Download directory for dbCAN databases
         pattern: "dbcan_db"
+  versions_rundbcan:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - rundbcan:
+          type: string
+          description: The name of the tool
+      - "run_dbcan version | sed 's/dbCAN version: //g'":
+          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
+      - rundbcan:
+          type: string
+          description: The name of the tool
+      - "run_dbcan version | sed 's/dbCAN version: //g'":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@Xinpeng021001"
 maintainers:

modules/nf-core/rundbcan/database/tests/main.nf.test

@@ -21,11 +21,9 @@ nextflow_process {
         then {
             assert process.success
             assert path(process.out.dbcan_db.get(0)).exists()
-            assert path(process.out.versions[0]).exists()
             assertAll(
                 { assert snapshot(
-                    process.out.versions,
-                    path(process.out.versions[0]).yaml
+                    process.out.findAll { key, val -> key.startsWith('versions') }
                 ).match() }
             )
         }
@@ -47,8 +45,7 @@ nextflow_process {
             assertAll(
                 { assert snapshot(
                     file(process.out.dbcan_db.get(0)).name,
-                    process.out.versions,
-                    path(process.out.versions[0]).yaml
+                    process.out.findAll { key, val -> key.startsWith('versions') }
                 ).match() }
             )
         }