Update bakta modules

CHANGELOG.md

@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#431](https://github.com/nf-core/funcscan/pull/431) Updated AMPcombi, Macrel, all MMseqs2 modules, MultiQC, Pyrodigal, and seqkit, added `--taxa_classification_mmseqs_compressed` parameter. (by @jasmezz)
 - [#438](https://github.com/nf-core/funcscan/pull/438) Updated to nf-core template 3.1.2. (by @jfy133)
 - [#441](https://github.com/nf-core/funcscan/pull/441) Updated to nf-core template 3.2.0, updated MultiQC. (by @jasmezz and @jfy133)
+- [#440](https://github.com/nf-core/funcscan/pull/440) Updated Bakta and introduced new parameter `--annotation_bakta_hmms`. (by @jasmezz)
 
 ### `Fixed`
 
@@ -27,6 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | Tool      | Previous version | New version |
 | --------- | ---------------- | ----------- |
 | AMPcombi  | 0.2.2            | 2.0.1       |
+| Bakta     | 1.9.3            | 1.10.4      |
 | Macrel    | 1.2.0            | 1.4.0       |
 | MMseqs2   | 15.6f452         | 17.b804f    |
 | MultiQC   | 1.24.0           | 1.27        |

conf/modules.config

@@ -168,6 +168,7 @@ process {
             params.annotation_bakta_gap ? '' : '--skip-gap',
             params.annotation_bakta_ori ? '' : '--skip-ori',
             params.annotation_bakta_activate_plot ? '' : '--skip-plot',
+            params.annotation_bakta_hmms ? '--hmms ${params.annotation_bakta_hmms}' : '',
         ].join(' ').trim()
     }
 

modules.json

@@ -62,12 +62,12 @@
                     },
                     "bakta/bakta": {
                         "branch": "master",
-                        "git_sha": "0e9cb409c32d3ec4f0d3804588e4778971c09b7e",
+                        "git_sha": "4f0998ebd8f65961cfef0b810f008be3bc477132",
                         "installed_by": ["modules"]
                     },
                     "bakta/baktadbdownload": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "4f0998ebd8f65961cfef0b810f008be3bc477132",
                         "installed_by": ["modules"]
                     },
                     "deeparg/downloaddata": {

nextflow.config

@@ -88,6 +88,7 @@ params {
     annotation_bakta_gap                            = false
     annotation_bakta_ori                            = false
     annotation_bakta_activate_plot                  = false
+    annotation_bakta_hmms                           = null
 
     annotation_prokka_singlemode                    = false
     annotation_prokka_rawproduct                    = false

nextflow_schema.json

@@ -352,6 +352,12 @@
                     "fa_icon": "fas fa-chart-pie",
                     "description": "Activate generation of circular genome plots.",
                     "help_text": "Activate this flag to generate genome plots (might be memory-intensive).\n\n>  Modifies tool parameter(s):\n> - BAKTA: `--skip-plot`"
+                },
+                "annotation_bakta_hmms": {
+                    "type": "string",
+                    "description": "Supply a path of an HMM file of trusted hidden markov models in HMMER format for CDS annotation",
+                    "help_text": "Bakta accepts user-provided trusted HMMs via `--hmms` in HMMER's text format. If set, Bakta will adhere to the *trusted cutoff* specified in the HMM header. In addition, a max. evalue threshold of 1e-6 is applied. For more info please refer to the BAKTA [documentation](https://github.com/oschwengers/bakta).\n\n>  Modifies tool parameter(s):\n> - BAKTA: `--hmms`",
+                    "fa_icon": "fa-regular fa-square-check"
                 }
             },
             "fa_icon": "fas fa-file-signature"

tests/test_bakta.nf.test

@@ -53,7 +53,7 @@ nextflow_pipeline {
                 ).match("macrel") },
 
                 // AMPcombi
-                { assert path("$outputDir/reports/ampcombi2/Ampcombi_summary.tsv").text.contains("KKEJHB_00100") },
+                { assert path("$outputDir/reports/ampcombi2/Ampcombi_summary.tsv").text.contains("KDEMFK_0115") },
                 { assert snapshot(
                     path("$outputDir/reports/ampcombi2/Ampcombi_cluster.log"),
                     path("$outputDir/reports/ampcombi2/Ampcombi_complete.log"),

tests/test_bakta.nf.test.snap

@@ -47,7 +47,7 @@
     "deeparg_tsv_ARG": {
         "content": [
             "sample_1.align.daa.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
-            "sample_2.align.daa.tsv:md5,4a86ca69defa4c861fabf236609afe8a",
+            "sample_2.align.daa.tsv:md5,4557fadca3f90ccb037b59558dddd528",
             "sample_1.mapping.ARG:md5,0e049e99eab4c55666062df21707d5b9",
             "sample_2.mapping.ARG:md5,0e049e99eab4c55666062df21707d5b9"
         ],

tests/test_taxonomy_bakta.nf.test

@@ -23,16 +23,16 @@ nextflow_pipeline {
 
                 // ampir
                 { assert snapshot(
-                    file("$outputDir/amp/ampir/sample_1/sample_1.ampir.tsv").text.contains("KKEJHB_00005"),
-                    file("$outputDir/amp/ampir/sample_1/sample_1.ampir.faa").text.contains("KKEJHB_00005"),
-                    file("$outputDir/amp/ampir/sample_2/sample_2.ampir.tsv").text.contains("KDEMFK_00005"),
-                    file("$outputDir/amp/ampir/sample_2/sample_2.ampir.faa").text.contains("KDEMFK_00005")
+                    file("$outputDir/amp/ampir/sample_1/sample_1.ampir.tsv").text.contains("KKEJHB_005"),
+                    file("$outputDir/amp/ampir/sample_1/sample_1.ampir.faa").text.contains("KKEJHB_005"),
+                    file("$outputDir/amp/ampir/sample_2/sample_2.ampir.tsv").text.contains("KDEMFK_0005"),
+                    file("$outputDir/amp/ampir/sample_2/sample_2.ampir.faa").text.contains("KDEMFK_0005")
                 ).match("ampir") },
 
                 // AMPlify
                 { assert snapshot(
-                    file("$outputDir/amp/amplify/sample_1/sample_1.amplify.tsv").text.contains("KKEJHB_00005"),
-                    file("$outputDir/amp/amplify/sample_2/sample_2.amplify.tsv").text.contains("KDEMFK_00005")
+                    file("$outputDir/amp/amplify/sample_1/sample_1.amplify.tsv").text.contains("KKEJHB_005"),
+                    file("$outputDir/amp/amplify/sample_2/sample_2.amplify.tsv").text.contains("KDEMFK_0005")
                 ).match("amplify") },
 
                 // Macrel
@@ -55,7 +55,7 @@ nextflow_pipeline {
 
                 // AMPcombi
                 { assert snapshot (
-                    file("$outputDir/reports/ampcombi2/sample_2/sample_2_ampcombi.tsv").text.contains("KDEMFK_00575"),
+                    file("$outputDir/reports/ampcombi2/sample_2/sample_2_ampcombi.tsv").text.contains("KDEMFK_0070"),
                 ).match("ampcombi") },
                 { assert new File("$outputDir/reports/ampcombi2/ampcombi_complete_summary_taxonomy.tsv.gz").exists() },