Update bakta modules to 1.120

modules/nf-core/bakta/bakta/environment.yml

@@ -4,4 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bakta=1.11.4
+  - bioconda::bakta=1.12.0
+  - bioconda::diamond=2.2.0

modules/nf-core/bakta/bakta/main.nf

@@ -4,8 +4,8 @@ process BAKTA_BAKTA {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
-        ? 'https://depot.galaxyproject.org/singularity/bakta:1.11.4--pyhdfd78af_0'
-        : 'quay.io/biocontainers/bakta:1.11.4--pyhdfd78af_0'}"
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/50/50b75335f6394ae83fd05f364db27ee2eb75f4170e3525bb2aea47ad717a9e64/data'
+        : 'community.wave.seqera.io/library/bakta_diamond:7830b94718da4f96'}"
 
     input:
     tuple val(meta), path(fasta)
@@ -26,7 +26,7 @@ process BAKTA_BAKTA {
     tuple val(meta), path("${prefix}.hypotheticals.faa"), emit: hypotheticals_faa
     tuple val(meta), path("${prefix}.tsv"), emit: tsv
     tuple val(meta), path("${prefix}.txt"), emit: txt
-    tuple val("${task.process}"), val('bakta'), eval("bakta --version 2>&1 | sed 's/bakta //'"), emit: versions_bakta, topic: versions
+    tuple val("${task.process}"), val('bakta'), eval("bakta --version 2>&1 | sed 's/.*bakta //'"), emit: versions_bakta, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -40,7 +40,9 @@ process BAKTA_BAKTA {
     def hmms_opt = hmms ? "--hmms ${hmms}" : ""
 
     """
-    export MPLCONFIGDIR=\$PWD/.matplotlib
+    ## Fake home due to fontconfig 'no writeable cache directory' issue
+    mkdir nxf_home
+    export HOME=\$PWD/nxf_home
 
     bakta \\
         ${fasta} \\
@@ -58,6 +60,9 @@ process BAKTA_BAKTA {
     prefix = task.ext.prefix ?: "${meta.id}"
     """
     export MPLCONFIGDIR=\$PWD/.matplotlib
+    export FONTCONFIG_PATH=\$PWD/.fontconfig
+    export XDG_CACHE_HOME=\$PWD/.cache
+    mkdir .fontconfig .cache
 
     touch ${prefix}.embl
     touch ${prefix}.faa

modules/nf-core/bakta/bakta/meta.yml

@@ -6,8 +6,7 @@ keywords:
   - bacteria
 tools:
   - bakta:
-      description: Rapid & standardized annotation of bacterial genomes, MAGs &
-        plasmids.
+      description: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids.
       homepage: https://github.com/oschwengers/bakta
       documentation: https://github.com/oschwengers/bakta
       tool_dev_url: https://github.com/oschwengers/bakta
@@ -27,38 +26,37 @@ input:
           FASTA file to be annotated. Has to contain at least a non-empty string dummy value.
         pattern: "*.{fa,fas,fna,fasta}"
         ontologies:
-          - edam: http://edamontology.org/format_1929 # FASTA
+          - edam: http://edamontology.org/format_1929
   - db:
       type: file
       description: |
         Path to the Bakta database directory. Must have amrfinderplus database directory already installed within it (in a directory called 'amrfinderplus-db/').
       ontologies:
-        - edam: http://edamontology.org/data_1049 # Directory name
+        - edam: http://edamontology.org/data_1049
   - proteins:
       type: file
-      description: FASTA/GenBank file of trusted proteins to first annotate from
-        (optional)
+      description: FASTA/GenBank file of trusted proteins to first annotate from (optional)
       pattern: "*.{fa,fas,fna,fasta,faa}"
       ontologies:
-        - edam: http://edamontology.org/format_1929 # FASTA
+        - edam: http://edamontology.org/format_1929
   - prodigal_tf:
       type: file
       description: Training file to use for Prodigal for CDS prediction(optional)
       pattern: "*.{tf,trn}"
       ontologies:
-        - edam: http://edamontology.org/format_2333 # Binary format
+        - edam: http://edamontology.org/format_2333
   - regions:
       type: file
       description: GFF3 or GenBank file of pre-annotated regions (optional)
       pattern: "*.{gbff,gff3}"
       ontologies:
-        - edam: http://edamontology.org/format_2206 # Sequence feature table format (text)
+        - edam: http://edamontology.org/format_2206
   - hmms:
       type: file
       description: HMM database file for custom annotation (optional)
       pattern: "*.hmm"
       ontologies:
-        - edam: http://edamontology.org/format_1370 # HMMER database format
+        - edam: http://edamontology.org/format_1370
 output:
   embl:
     - - meta:
@@ -71,7 +69,7 @@ output:
           description: annotations & sequences in (multi) EMBL format
           pattern: "*.embl"
           ontologies:
-            - edam: http://edamontology.org/format_1927 # EMBL format
+            - edam: http://edamontology.org/format_1927
   faa:
     - - meta:
           type: map
@@ -83,7 +81,7 @@ output:
           description: CDS/sORF amino acid sequences as FASTA
           pattern: "*.faa"
           ontologies:
-            - edam: http://edamontology.org/format_1929 # FASTA
+            - edam: http://edamontology.org/format_1929
   ffn:
     - - meta:
           type: map
@@ -95,7 +93,7 @@ output:
           description: feature nucleotide sequences as FASTA
           pattern: "*.ffn"
           ontologies:
-            - edam: http://edamontology.org/format_1929 # FASTA
+            - edam: http://edamontology.org/format_1929
   fna:
     - - meta:
           type: map
@@ -107,7 +105,7 @@ output:
           description: replicon/contig DNA sequences as FASTA
           pattern: "*.fna"
           ontologies:
-            - edam: http://edamontology.org/format_1929 # FASTA
+            - edam: http://edamontology.org/format_1929
   gbff:
     - - meta:
           type: map
@@ -119,7 +117,7 @@ output:
           description: annotations & sequences in (multi) GenBank format
           pattern: "*.gbff"
           ontologies:
-            - edam: http://edamontology.org/format_1936 # GenBank format
+            - edam: http://edamontology.org/format_1936
   gff:
     - - meta:
           type: map
@@ -131,7 +129,7 @@ output:
           description: annotations & sequences in GFF3 format
           pattern: "*.gff3"
           ontologies:
-            - edam: http://edamontology.org/format_1975 # GFF3 format
+            - edam: http://edamontology.org/format_1975
   hypotheticals_tsv:
     - - meta:
           type: map
@@ -140,11 +138,11 @@ output:
             e.g. [ id:'test', single_end:false ]
       - ${prefix}.hypotheticals.tsv:
           type: file
-          description: additional information on hypothetical protein CDS as
-            simple human readable tab separated values
+          description: additional information on hypothetical protein CDS as simple
+            human readable tab separated values
           pattern: "*.hypotheticals.tsv"
           ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+            - edam: http://edamontology.org/format_3475
   hypotheticals_faa:
     - - meta:
           type: map
@@ -156,7 +154,7 @@ output:
           description: hypothetical protein CDS amino acid sequences as FASTA
           pattern: "*.hypotheticals.faa"
           ontologies:
-            - edam: http://edamontology.org/format_1929 # FASTA
+            - edam: http://edamontology.org/format_1929
   tsv:
     - - meta:
           type: map
@@ -168,7 +166,7 @@ output:
           description: annotations as simple human readable tab separated values
           pattern: "*.tsv"
           ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+            - edam: http://edamontology.org/format_3475
   txt:
     - - meta:
           type: map
@@ -180,15 +178,15 @@ output:
           description: genome statistics and annotation summary
           pattern: "*.txt"
           ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+            - edam: http://edamontology.org/format_3475
   versions_bakta:
     - - ${task.process}:
           type: string
           description: The name of the process
       - bakta:
           type: string
           description: The name of the tool
-      - bakta --version 2>&1 | sed 's/bakta //':
+      - bakta --version 2>&1 | sed 's/.*bakta //':
           type: eval
           description: The expression to obtain the version of the tool
 topics:
@@ -199,7 +197,7 @@ topics:
       - bakta:
           type: string
           description: The name of the tool
-      - bakta --version 2>&1 | sed 's/bakta //':
+      - bakta --version 2>&1 | sed 's/.*bakta //':
           type: eval
           description: The expression to obtain the version of the tool
 authors:

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

@@ -6,15 +6,15 @@
                     [
                         "BAKTA_BAKTA",
                         "bakta",
-                        "1.11.4"
+                        "1.12.0"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-03-17T21:20:19.285606344",
+        "timestamp": "2026-06-17T15:40:47.396215774",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "26.02.0"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     },
     "Bakta - stub": {
@@ -104,15 +104,15 @@
                     [
                         "BAKTA_BAKTA",
                         "bakta",
-                        "1.11.4"
+                        "1.12.0"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-03-17T21:20:30.005281737",
+        "timestamp": "2026-06-17T12:15:36.61419838",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "26.02.0"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     }
 }

modules/nf-core/bakta/baktadbdownload/environment.yml

@@ -4,4 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bakta=1.11.4
+  - bioconda::bakta=1.12.0
+  - bioconda::diamond=2.2.0

modules/nf-core/bakta/baktadbdownload/main.nf

@@ -3,20 +3,22 @@ process BAKTA_BAKTADBDOWNLOAD {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
-        ? 'https://depot.galaxyproject.org/singularity/bakta:1.11.4--pyhdfd78af_0'
-        : 'quay.io/biocontainers/bakta:1.11.4--pyhdfd78af_0'}"
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/50/50b75335f6394ae83fd05f364db27ee2eb75f4170e3525bb2aea47ad717a9e64/data'
+        : 'community.wave.seqera.io/library/bakta_diamond:7830b94718da4f96'}"
 
     output:
     path "db*", emit: db
-    tuple val("${task.process}"), val('bakta'), eval("bakta --version 2>&1 | sed 's/bakta //'"), emit: versions_bakta, topic: versions
+    tuple val("${task.process}"), val('bakta'), eval("bakta --version 2>&1 | sed 's/.*bakta //'"), emit: versions_bakta, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
     """
-    export MPLCONFIGDIR=\$PWD/.matplotlib
+    ## Fake home due to fontconfig 'no writeable cache directory' issue
+    mkdir nxf_home
+    export HOME=\$PWD/nxf_home
 
     bakta_db \\
         download \\
@@ -27,6 +29,9 @@ process BAKTA_BAKTADBDOWNLOAD {
     def args = task.ext.args ?: ''
     """
     export MPLCONFIGDIR=\$PWD/.matplotlib
+    export FONTCONFIG_PATH=\$PWD/.fontconfig
+    export XDG_CACHE_HOME=\$PWD/.cache
+    mkdir .fontconfig .cache
 
     echo "bakta_db \\
         download \\

modules/nf-core/bakta/baktadbdownload/meta.yml

@@ -9,8 +9,7 @@ keywords:
   - download
 tools:
   - bakta:
-      description: Rapid & standardized annotation of bacterial genomes, MAGs &
-        plasmids
+      description: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
       homepage: https://github.com/oschwengers/bakta
       documentation: https://github.com/oschwengers/bakta
       tool_dev_url: https://github.com/oschwengers/bakta
@@ -32,7 +31,7 @@ output:
       - bakta:
           type: string
           description: The name of the tool
-      - bakta --version 2>&1 | sed 's/bakta //':
+      - bakta --version 2>&1 | sed 's/.*bakta //':
           type: eval
           description: The expression to obtain the version of the tool
 topics:
@@ -43,7 +42,7 @@ topics:
       - bakta:
           type: string
           description: The name of the tool
-      - bakta --version 2>&1 | sed 's/bakta //':
+      - bakta --version 2>&1 | sed 's/.*bakta //':
           type: eval
           description: The expression to obtain the version of the tool
 authors:

modules/nf-core/bakta/baktadbdownload/tests/main.nf.test.snap

@@ -6,15 +6,15 @@
                     [
                         "BAKTA_BAKTADBDOWNLOAD",
                         "bakta",
-                        "1.11.4"
+                        "1.12.0"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-03-17T21:23:17.513160347",
+        "timestamp": "2026-06-18T14:36:06.696663407",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "26.02.0"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     },
     "Bakta database download - stub": {
@@ -30,15 +30,15 @@
                     [
                         "BAKTA_BAKTADBDOWNLOAD",
                         "bakta",
-                        "1.11.4"
+                        "1.12.0"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-03-18T10:36:34.397679686",
+        "timestamp": "2026-06-18T14:36:14.006059546",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "26.02.0"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     }
 }